Qiang Cheng

Xinxing Wu, Chong Peng, Peter T. Nelson et al.

Alzheimer's disease (AD), as a progressive brain disease, affects cognition, memory, and behavior. Similarly, limbic-predominant age-related TDP-43 encephalopathy (LATE) is a recently defined common neurodegenerative disease that mimics the clinical symptoms of AD. At present, the risk factors implicated in LATE and those distinguishing LATE from AD are largely unknown. We leveraged an integrated feature selection-based algorithmic approach, to identify important factors differentiating subjects with LATE and/or AD from Control on significantly imbalanced data. We analyzed two datasets ROSMAP and NACC and discovered that alcohol consumption was a top lifestyle and environmental factor linked with LATE and AD and their associations were differential. In particular, we identified a specific subpopulation consisting of APOE e4 carriers. We found that, for this subpopulation, light-to-moderate alcohol intake was a protective factor against both AD and LATE, but its protective role against AD appeared stronger than LATE. The codes for our algorithms are available at https://github.com/xinxingwu-uk/PFV.

Xinxing Wu, Chong Peng, Gregory Jicha et al.

The disruption of circadian rhythm is a cardinal symptom for Alzheimer's disease (AD) patients. The full circadian rhythm orchestration of gene expression in the human brain and its inherent associations with AD remain largely unknown. We present a novel comprehensive approach, PRIME, to detect and analyze rhythmic oscillation patterns in untimed high-dimensional gene expression data across multiple datasets. To demonstrate the utility of PRIME, firstly, we validate it by a time course expression dataset from mouse liver as a cross-species and cross-organ validation. Then, we apply it to study oscillation patterns in untimed genome-wide gene expression from 19 human brain regions of controls and AD patients. Our findings reveal clear, synchronized oscillation patterns in 15 pairs of brain regions of control, while these oscillation patterns either disappear or dim for AD. It is worth noting that PRIME discovers the circadian rhythmic patterns without requiring the sample's timestamps. The codes for PRIME, along with codes to reproduce the figures in this paper, are available at https://github.com/xinxingwu-uk/PRIME.

Chong Peng, Yiqun Zhang, Yongyong Chen et al.

Nonnegative matrix factorization (NMF) has been widely studied in recent years due to its effectiveness in representing nonnegative data with parts-based representations. For NMF, a sparser solution implies better parts-based representation.However, current NMF methods do not always generate sparse solutions.In this paper, we propose a new NMF method with log-norm imposed on the factor matrices to enhance the sparseness.Moreover, we propose a novel column-wisely sparse norm, named $\ell_{2,\log}$-(pseudo) norm to enhance the robustness of the proposed method.The $\ell_{2,\log}$-(pseudo) norm is invariant, continuous, and differentiable.For the $\ell_{2,\log}$ regularized shrinkage problem, we derive a closed-form solution, which can be used for other general problems.Efficient multiplicative updating rules are developed for the optimization, which theoretically guarantees the convergence of the objective value sequence.Extensive experimental results confirm the effectiveness of the proposed method, as well as the enhanced sparseness and robustness.

Xinxing Wu, Chong Peng, Richard Charnigo et al.

Interpreting critical variables involved in complex biological processes related to survival time can help understand prediction from survival models, evaluate treatment efficacy, and develop new therapies for patients. Currently, the predictive results of deep learning (DL)-based models are better than or as good as standard survival methods, they are often disregarded because of their lack of transparency and little interpretability, which is crucial to their adoption in clinical applications. In this paper, we introduce a novel, easily deployable approach, called EXplainable CEnsored Learning (EXCEL), to iteratively exploit critical variables and simultaneously implement (DL) model training based on these variables. First, on a toy dataset, we illustrate the principle of EXCEL; then, we mathematically analyze our proposed method, and we derive and prove tight generalization error bounds; next, on two semi-synthetic datasets, we show that EXCEL has good anti-noise ability and stability; finally, we apply EXCEL to a variety of real-world survival datasets including clinical data and genetic data, demonstrating that EXCEL can effectively identify critical features and achieve performance on par with or better than the original models. It is worth pointing out that EXCEL is flexibly deployed in existing or emerging models for explainable survival data in the presence of right censoring.

Md Atik Ahamed, Mihir Parmar, Palash Goyal et al.

We introduce TFRBench, the first benchmark designed to evaluate the reasoning capabilities of forecasting systems. Traditionally, time-series forecasting has been evaluated solely on numerical accuracy, treating foundation models as ``black boxes.'' Unlike existing benchmarks, TFRBench provides a protocol for evaluating the reasoning generated by forecasting systems--specifically their analysis of cross-channel dependencies, trends, and external events. To enable this, we propose a systematic multi-agent framework that utilizes an iterative verification loop to synthesize numerically grounded reasoning traces. Spanning ten datasets across five domains, our evaluation confirms that this reasoning is causally effective; useful for evaluation; and prompting LLMs with our generated traces significantly improves forecasting accuracy compared to direct numerical prediction (e.g., avg. $\sim40.2\%\to56.6\%)$, validating the quality of our reasoning. Conversely, benchmarking experiments reveal that off-the-shelf LLMs consistently struggle with both reasoning (lower LLM-as-a-Judge scores) and numerical forecasting, frequently failing to capture domain-specific dynamics. TFRBench thus establishes a new standard for interpretable, reasoning-based evaluation in time-series forecasting. Our benchmark is available at: https://tfrbench.github.io

Sania Eskandari, Ali Eslamian, Nusrat Munia et al.

This study evaluates the effectiveness of deep learning models in classifying histopathological images for early and accurate detection of breast cancer. Eight advanced models, including ResNet-50, DenseNet-121, ResNeXt-50, Vision Transformer (ViT), GoogLeNet (Inception v3), EfficientNet, MobileNet, and SqueezeNet, were compared using a dataset of 277,524 image patches. The Vision Transformer (ViT) model, with its attention-based mechanisms, achieved the highest validation accuracy of 94%, outperforming conventional CNNs. The study demonstrates the potential of advanced machine learning methods to enhance precision and efficiency in breast cancer diagnosis in clinical settings.

Ling Team, Anqi Shen, Baihui Li et al.

We present Ring-1T, the first open-source, state-of-the-art thinking model with a trillion-scale parameter. It features 1 trillion total parameters and activates approximately 50 billion per token. Training such models at a trillion-parameter scale introduces unprecedented challenges, including train-inference misalignment, inefficiencies in rollout processing, and bottlenecks in the RL system. To address these, we pioneer three interconnected innovations: (1) IcePop stabilizes RL training via token-level discrepancy masking and clipping, resolving instability from training-inference mismatches; (2) C3PO++ improves resource utilization for long rollouts under a token budget by dynamically partitioning them, thereby obtaining high time efficiency; and (3) ASystem, a high-performance RL framework designed to overcome the systemic bottlenecks that impede trillion-parameter model training. Ring-1T delivers breakthrough results across critical benchmarks: 93.4 on AIME-2025, 86.72 on HMMT-2025, 2088 on CodeForces, and 55.94 on ARC-AGI-1. Notably, it attains a silver medal-level result on the IMO-2025, underscoring its exceptional reasoning capabilities. By releasing the complete 1T parameter MoE model to the community, we provide the research community with direct access to cutting-edge reasoning capabilities. This contribution marks a significant milestone in democratizing large-scale reasoning intelligence and establishes a new baseline for open-source model performance.

Md Atik Ahamed, Qiang Cheng

Long-term time-series forecasting remains challenging due to the difficulty in capturing long-term dependencies, achieving linear scalability, and maintaining computational efficiency. We introduce TimeMachine, an innovative model that leverages Mamba, a state-space model, to capture long-term dependencies in multivariate time series data while maintaining linear scalability and small memory footprints. TimeMachine exploits the unique properties of time series data to produce salient contextual cues at multi-scales and leverage an innovative integrated quadruple-Mamba architecture to unify the handling of channel-mixing and channel-independence situations, thus enabling effective selection of contents for prediction against global and local contexts at different scales. Experimentally, TimeMachine achieves superior performance in prediction accuracy, scalability, and memory efficiency, as extensively validated using benchmark datasets. Code availability: https://github.com/Atik-Ahamed/TimeMachine

Aram Ansary Ogholbake, Hannah Choi, Spencer Brandenburg et al.

We propose AttentionMixer, a unified deep learning framework for multimodal detection of brain edema that combines structural head CT (HCT) with routine clinical metadata. While HCT provides rich spatial information, clinical variables such as age, laboratory values, and scan timing capture complementary context that might be ignored or naively concatenated. AttentionMixer is designed to fuse these heterogeneous sources in a principled and efficient manner. HCT volumes are first encoded using a self-supervised Vision Transformer Autoencoder (ViT-AE++), without requiring large labeled datasets. Clinical metadata are mapped into the same feature space and used as keys and values in a cross-attention module, where HCT-derived feature vector serves as queries. This cross-attention fusion allows the network to dynamically modulate imaging features based on patient-specific context and provides an interpretable mechanism for multimodal integration. A lightweight MLP-Mixer then refines the fused representation before final classification, enabling global dependency modeling with substantially reduced parameter overhead. Missing or incomplete metadata are handled via a learnable embedding, promoting robustness to real-world clinical data quality. We evaluate AttentionMixer on a curated brain HCT cohort with expert edema annotations using five-fold cross-validation. Compared with strong HCT-only, metadata-only, and prior multimodal baselines, AttentionMixer achieves superior performance (accuracy 87.32%, precision 92.10%, F1-score 85.37%, AUC 94.14%). Ablation studies confirm the benefit of both cross-attention and MLP-Mixer refinement, and permutation-based metadata importance analysis highlights clinically meaningful variables driving predictions. These results demonstrate that structured, interpretable multimodal fusion can substantially improve edema detection in clinical practice.

Md Atik Ahamed, Mihir Parmar, Palash Goyal et al.

Time Series Foundation Models (TSFMs) excel at numerical forecasting but operate as black boxes lacking qualitative reasoning. Conversely, applying LLMs directly to temporal data introduces a modality gap: text tokenizers fragment continuous numerical values, degrading mathematical relationships and exploding sequence lengths, leading to computational overhead. To resolve this, we introduce STRIDE (Strategic Time-series Reasoning Injected via Distilled Embeddings), a novel framework natively integrating LLM reasoning into the continuous embedding space of TSFMs. Instead of discrete tokens, STRIDE distills reasoning traces into a lightweight LLM, dynamically projecting its mean-pooled hidden states as a cross-modal prior into the target numerical encoder. The architecture is jointly optimized using cross-entropy and quantile losses. Evaluations demonstrate STRIDE establishes state-of-the-art numerical forecasting on GIFT-Eval (0.674 MASE, 0.454 CRPS) compared to TSFMs and exhibits superior in-domain and out-of-domain numerical as well as reasoning performance on TFRBench. Specifically, STRIDE acts as a plug-and-play enhancement, consistently improving diverse TSFMs (e.g., Chronos-2, Timer-S1) across various LLM configurations. Thus, injecting semantic reasoning as a continuous prior equips TSFMs with human-interpretable reasoning while fundamentally improving predictive accuracy.

Shuang Ge, Shuqing Sun, Huan Xu et al.

The development of single-cell and spatial transcriptomics has revolutionized our capacity to investigate cellular properties, functions, and interactions in both cellular and spatial contexts. However, the analysis of single-cell and spatial omics data remains challenging. First, single-cell sequencing data are high-dimensional and sparse, often contaminated by noise and uncertainty, obscuring the underlying biological signals. Second, these data often encompass multiple modalities, including gene expression, epigenetic modifications, and spatial locations. Integrating these diverse data modalities is crucial for enhancing prediction accuracy and biological interpretability. Third, while the scale of single-cell sequencing has expanded to millions of cells, high-quality annotated datasets are still limited. Fourth, the complex correlations of biological tissues make it difficult to accurately reconstruct cellular states and spatial contexts. Traditional feature engineering-based analysis methods struggle to deal with the various challenges presented by intricate biological networks. Deep learning has emerged as a powerful tool capable of handling high-dimensional complex data and automatically identifying meaningful patterns, offering significant promise in addressing these challenges. This review systematically analyzes these challenges and discusses related deep learning approaches. Moreover, we have curated 21 datasets from 9 benchmarks, encompassing 58 computational methods, and evaluated their performance on the respective modeling tasks. Finally, we highlight three areas for future development from a technical, dataset, and application perspective. This work will serve as a valuable resource for understanding how deep learning can be effectively utilized in single-cell and spatial transcriptomics analyses, while inspiring novel approaches to address emerging challenges.

Ali Eslamian, Alireza Afzal Aghaei, Qiang Cheng

Tabular data analysis presents unique challenges due to its heterogeneous feature types, missing values, and complex interactions. While traditional machine learning methods, such as gradient boosting, often outperform deep learning approaches, recent advancements in neural architectures offer promising alternatives. This paper introduces TabKAN, a novel framework that advances tabular data modeling using Kolmogorov-Arnold Networks (KANs). Unlike conventional deep learning models, KANs leverge learnable activation functions on edges, which improve both interpretability and training efficiency. Our contributions include: (1) the introduction of modular KAN-based architectures for tabular data analysis, (2) the development of a transfer learning framework for KAN models that supports knowledge transfer between domains, (3) the development of model-specific interpretability for tabular data learning, which reduces dependence on post hoc and model-agnostic analysis, and (4) comprehensive evaluation of vanilla supervised learning across binary and multi-class classification tasks. Through extensive benchmarking on diverse public datasets, TabKAN demonstrates superior performance in supervised learning while significantly outperforming classical and Transformer-based models in transfer learning scenarios. Our findings highlight the advantage of KAN-based architectures in transferring knowledge across domains and narrowing the gap between traditional machine learning and deep learning for structured data.

Ali Eslamian, Qiang Cheng

Tabular data poses unique challenges for deep learning due to its heterogeneous feature types, lack of spatial structure, and often limited sample sizes. We propose TabNSA, a novel deep learning framework that integrates Native Sparse Attention (NSA) with a TabMixer backbone to efficiently model tabular data. TabNSA tackles computational and representational challenges by dynamically focusing on relevant feature subsets per instance. The NSA module employs a hierarchical sparse attention mechanism, including token compression, selective preservation, and localized sliding windows, to significantly reduce the quadratic complexity of standard attention operations while addressing feature heterogeneity. Complementing this, the TabMixer backbone captures complex, non-linear dependencies through parallel multilayer perceptron (MLP) branches with independent parameters. These modules are synergistically combined via element-wise summation and mean pooling, enabling TabNSA to model both global context and fine-grained interactions. Extensive experiments across supervised and transfer learning settings show that TabNSA consistently outperforms state-of-the-art deep learning models. Furthermore, by augmenting TabNSA with a fine-tuned large language model (LLM), we enable it to effectively address Few-Shot Learning challenges through language-guided generalization on diverse tabular benchmarks.

Rabeya Tus Sadia, Md Atik Ahamed, Qiang Cheng

The integration of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) data is crucial for understanding gene expression in spatial context. Existing methods for such integration have limited performance, with structural similarity often below 60\%, We attribute this limitation to the failure to consider causal relationships between genes. We present CausalGeD, which combines diffusion and autoregressive processes to leverage these relationships. By generalizing the Causal Attention Transformer from image generation to gene expression data, our model captures regulatory mechanisms without predefined relationships. Across 10 tissue datasets, CausalGeD outperformed state-of-the-art baselines by 5- 32\% in key metrics, including Pearson's correlation and structural similarity, advancing both technical and biological insights.

Xin Tong, Bo Jin, Zhi Lin et al.

Large Language Models (LLMs) have demonstrated significant potential and effectiveness across multiple application domains. To assess the performance of mainstream LLMs in public security tasks, this study aims to construct a specialized evaluation benchmark tailored to the Chinese public security domain--CPSDbench. CPSDbench integrates datasets related to public security collected from real-world scenarios, supporting a comprehensive assessment of LLMs across four key dimensions: text classification, information extraction, question answering, and text generation. Furthermore, this study introduces a set of innovative evaluation metrics designed to more precisely quantify the efficacy of LLMs in executing tasks related to public security. Through the in-depth analysis and evaluation conducted in this research, we not only enhance our understanding of the performance strengths and limitations of existing models in addressing public security issues but also provide references for the future development of more accurate and customized LLM models targeted at applications in this field.

Rabeya Tus Sadia, Qiang Cheng

Predicting the success of start-up companies, defined as achieving an exit through acquisition or IPO, is a critical problem in entrepreneurship and innovation research. Datasets such as Crunchbase provide both structured information (e.g., funding rounds, industries, investor networks) and unstructured text (e.g., company descriptions), but effectively leveraging this heterogeneous data for prediction remains challenging. Traditional machine learning approaches often rely only on structured features and achieve moderate accuracy, while large language models (LLMs) offer rich reasoning abilities but struggle to adapt directly to domain-specific business data. We present \textbf{CrunchLLM}, a domain-adapted LLM framework for startup success prediction. CrunchLLM integrates structured company attributes with unstructured textual narratives and applies parameter-efficient fine-tuning strategies alongside prompt optimization to specialize foundation models for entrepreneurship data. Our approach achieves accuracy exceeding 80\% on Crunchbase startup success prediction, significantly outperforming traditional classifiers and baseline LLMs. Beyond predictive performance, CrunchLLM provides interpretable reasoning traces that justify its predictions, enhancing transparency and trustworthiness for financial and policy decision makers. This work demonstrates how adapting LLMs with domain-aware fine-tuning and structured--unstructured data fusion can advance predictive modeling of entrepreneurial outcomes. CrunchLLM contributes a methodological framework and a practical tool for data-driven decision making in venture capital and innovation policy.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

Molecular generation conditioned on textual descriptions is a fundamental task in computational chemistry and drug discovery. Existing methods often struggle to simultaneously ensure high-quality, diverse generation and fast inference. In this work, we propose a novel causality-aware framework that addresses these challenges through two key innovations. First, we introduce a Causality-Aware Transformer (CAT) that jointly encodes molecular graph tokens and text instructions while enforcing causal dependencies during generation. Second, we develop a Variational Mean Flow (VMF) framework that generalizes existing flow-based methods by modeling the latent space as a mixture of Gaussians, enhancing expressiveness beyond unimodal priors. VMF enables efficient one-step inference while maintaining strong generation quality and diversity. Extensive experiments on four standard molecular benchmarks demonstrate that our model outperforms state-of-the-art baselines, achieving higher novelty (up to 74.5\%), diversity (up to 70.3\%), and 100\% validity across all datasets. Moreover, VMF requires only one number of function evaluation (NFE) during conditional generation and up to five NFEs for unconditional generation, offering substantial computational efficiency over diffusion-based methods.

Rabeya Tus Sadia, Qiang Cheng

Microbiome data analysis is essential for understanding host health and disease, yet its inherent sparsity and noise pose major challenges for accurate imputation, hindering downstream tasks such as biomarker discovery. Existing imputation methods, including recent diffusion-based models, often fail to capture the complex interdependencies between microbial taxa and overlook contextual metadata that can inform imputation. We introduce DepMicroDiff, a novel framework that combines diffusion-based generative modeling with a Dependency-Aware Transformer (DAT) to explicitly capture both mutual pairwise dependencies and autoregressive relationships. DepMicroDiff is further enhanced by VAE-based pretraining across diverse cancer datasets and conditioning on patient metadata encoded via a large language model (LLM). Experiments on TCGA microbiome datasets show that DepMicroDiff substantially outperforms state-of-the-art baselines, achieving higher Pearson correlation (up to 0.712), cosine similarity (up to 0.812), and lower RMSE and MAE across multiple cancer types, demonstrating its robustness and generalizability for microbiome imputation.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

Missing values in high-dimensional, mixed-type datasets pose significant challenges for data imputation, particularly under Missing Not At Random (MNAR) mechanisms. Existing methods struggle to integrate local and global data characteristics, limiting performance in MNAR and high-dimensional settings. We propose an innovative framework, RefiDiff, combining local machine learning predictions with a novel Mamba-based denoising network efficiently capturing long-range dependencies among features and samples with low computational complexity. RefiDiff bridges the predictive and generative paradigms of imputation, leveraging pre-refinement for initial warm-up imputations and post-refinement to polish results, enhancing stability and accuracy. By encoding mixed-type data into unified tokens, RefiDiff enables robust imputation without architectural or hyperparameter tuning. RefiDiff outperforms state-of-the-art (SOTA) methods across missing-value settings, demonstrating strong performance in MNAR settings and superior out-of-sample generalization. Extensive evaluations on nine real-world datasets demonstrate its robustness, scalability, and effectiveness in handling complex missingness patterns.

Md Atik Ahamed, Qiang Ye, Qiang Cheng

The design of novel molecules with desired properties is a key challenge in drug discovery and materials science. Traditional methods rely on trial-and-error, while recent deep learning approaches have accelerated molecular generation. However, existing models struggle with generating molecules based on specific textual descriptions. We introduce Mol-CADiff, a novel diffusion-based framework that uses causal attention mechanisms for text-conditional molecular generation. Our approach explicitly models the causal relationship between textual prompts and molecular structures, overcoming key limitations in existing methods. We enhance dependency modeling both within and across modalities, enabling precise control over the generation process. Our extensive experiments demonstrate that Mol-CADiff outperforms state-of-the-art methods in generating diverse, novel, and chemically valid molecules, with better alignment to specified properties, enabling more intuitive language-driven molecular design.

Md Atik Ahamed, Andrew Cheng, Qiang Ye et al.

Graph Neural Networks (GNNs) have demonstrated remarkable success in various applications, yet they often struggle to capture long-range dependencies (LRD) effectively. This paper introduces GraphMinNet, a novel GNN architecture that generalizes the idea of minimal Gated Recurrent Units to graph-structured data. Our approach achieves efficient LRD modeling with linear computational complexity while maintaining permutation equivariance and stability. The model incorporates both structural and positional information through a unique combination of feature and positional encodings, leading to provably stronger expressiveness than the 1-WL test. Theoretical analysis establishes that GraphMinNet maintains non-decaying gradients over long distances, ensuring effective long-range information propagation. Extensive experiments on ten diverse datasets, including molecular graphs, image graphs, and synthetic networks, demonstrate that GraphMinNet achieves state-of-the-art performance while being computationally efficient. Our results show superior performance on 6 out of 10 datasets and competitive results on the others, validating the effectiveness of our approach in capturing both local and global graph structures.

Zhen Zhang, Jun Hui Qiu, Jun Wei Zhang et al.

Reconfigurable intelligent surface (RIS) is a two-dimensional periodic structure integrated with a large number of reflective elements, which can manipulate electromagnetic waves in a digital way, offering great potentials for wireless communication and radar detection applications. However, conventional RIS designs highly rely on extensive full-wave EM simulations that are extremely time-consuming. To address this challenge, we propose a machine-learning-assisted approach for efficient RIS design. An accurate and fast model to predict the reflection coefficient of RIS element is developed by combining a multi-layer perceptron neural network (MLP) and a dual-port network, which can significantly reduce tedious EM simulations in the network training. A RIS has been practically designed based on the proposed method. To verify the proposed method, the RIS has also been fabricated and measured. The experimental results are in good agreement with the simulation results, which validates the efficacy of the proposed method in RIS design.

Aram Ansary Ogholbake, Qiang Cheng

Circadian rhythms regulate the physiology and behavior of humans and animals. Despite advancements in understanding these rhythms and predicting circadian phases at the transcriptional level, predicting circadian phases from proteomic data remains elusive. This challenge is largely due to the scarcity of time labels in proteomic datasets, which are often characterized by small sample sizes, high dimensionality, and significant noise. Furthermore, existing methods for predicting circadian phases from transcriptomic data typically rely on prior knowledge of known rhythmic genes, making them unsuitable for proteomic datasets. To address this gap, we developed a novel computational method using unsupervised deep learning techniques to predict circadian sample phases from proteomic data without requiring time labels or prior knowledge of proteins or genes. Our model involves a two-stage training process optimized for robust circadian phase prediction: an initial greedy one-layer-at-a-time pre-training which generates informative initial parameters followed by fine-tuning. During fine-tuning, a specialized loss function guides the model to align protein expression levels with circadian patterns, enabling it to accurately capture the underlying rhythmic structure within the data. We tested our method on both time-labeled and unlabeled proteomic data. For labeled data, we compared our predictions to the known time labels, achieving high accuracy, while for unlabeled human datasets, including postmortem brain regions and urine samples, we explored circadian disruptions. Notably, our analysis identified disruptions in rhythmic proteins between Alzheimer's disease and control subjects across these samples.

Md Atik Ahamed, Qiang Cheng

Multivariate time series classification (TSC) is critical for various applications in fields such as healthcare and finance. While various approaches for TSC have been explored, important properties of time series, such as shift equivariance and inversion invariance, are largely underexplored by existing works. To fill this gap, we propose a novel multi-view approach to capture patterns with properties like shift equivariance. Our method integrates diverse features, including spectral, temporal, local, and global features, to obtain rich, complementary contexts for TSC. We use continuous wavelet transform to capture time-frequency features that remain consistent even when the input is shifted in time. These features are fused with temporal convolutional or multilayer perceptron features to provide complex local and global contextual information. We utilize the Mamba state space model for efficient and scalable sequence modeling and capturing long-range dependencies in time series. Moreover, we introduce a new scanning scheme for Mamba, called tango scanning, to effectively model sequence relationships and leverage inversion invariance, thereby enhancing our model's generalization and robustness. Experiments on two sets of benchmark datasets (10+20 datasets) demonstrate our approach's effectiveness, achieving average accuracy improvements of 4.01-6.45\% and 7.93\% respectively, over leading TSC models such as TimesNet and TSLANet.

Md Atik Ahamed, Qiang Cheng

Despite the prevalence of images and texts in machine learning, tabular data remains widely used across various domains. Existing deep learning models, such as convolutional neural networks and transformers, perform well however demand extensive preprocessing and tuning limiting accessibility and scalability. This work introduces an innovative approach based on a structured state-space model (SSM), MambaTab, for tabular data. SSMs have strong capabilities for efficiently extracting effective representations from data with long-range dependencies. MambaTab leverages Mamba, an emerging SSM variant, for end-to-end supervised learning on tables. Compared to state-of-the-art baselines, MambaTab delivers superior performance while requiring significantly fewer parameters, as empirically validated on diverse benchmark datasets. MambaTab's efficiency, scalability, generalizability, and predictive gains signify it as a lightweight, "plug-and-play" solution for diverse tabular data with promise for enabling wider practical applications.

Hua Lan, Jinjie Hu, Zengfu Wang et al.

Motivated by the maneuvering target tracking with sensors such as radar and sonar, this paper considers the joint and recursive estimation of the dynamic state and the time-varying process noise covariance in nonlinear state space models. Due to the nonlinearity of the models and the non-conjugate prior, the state estimation problem is generally intractable as it involves integrals of general nonlinear functions and unknown process noise covariance, resulting in the posterior probability distribution functions lacking closed-form solutions. This paper presents a recursive solution for joint nonlinear state estimation and model parameters identification based on the approximate Bayesian inference principle. The stochastic search variational inference is adopted to offer a flexible, accurate, and effective approximation of the posterior distributions. We make two contributions compared to existing variational inference-based noise adaptive filtering methods. First, we introduce an auxiliary latent variable to decouple the latent variables of dynamic state and process noise covariance, thereby improving the flexibility of the posterior inference. Second, we split the variational lower bound optimization into conjugate and non-conjugate parts, whereas the conjugate terms are directly optimized that admit a closed-form solution and the non-conjugate terms are optimized by natural gradients, achieving the trade-off between inference speed and accuracy. The performance of the proposed method is verified on radar target tracking applications by both simulated and real-world data.

Chong Peng, Yang Liu, Yongyong Chen et al.

In this paper, we propose a novel nonconvex approach to robust principal component analysis for HSI denoising, which focuses on simultaneously developing more accurate approximations to both rank and column-wise sparsity for the low-rank and sparse components, respectively. In particular, the new method adopts the log-determinant rank approximation and a novel $\ell_{2,\log}$ norm, to restrict the local low-rank or column-wisely sparse properties for the component matrices, respectively. For the $\ell_{2,\log}$-regularized shrinkage problem, we develop an efficient, closed-form solution, which is named $\ell_{2,\log}$-shrinkage operator. The new regularization and the corresponding operator can be generally used in other problems that require column-wise sparsity. Moreover, we impose the spatial-spectral total variation regularization in the log-based nonconvex RPCA model, which enhances the global piece-wise smoothness and spectral consistency from the spatial and spectral views in the recovered HSI. Extensive experiments on both simulated and real HSIs demonstrate the effectiveness of the proposed method in denoising HSIs.

Xinxing Wu, Qiang Cheng

Feature selection identifies subsets of informative features and reduces dimensions in the original feature space, helping provide insights into data generation or a variety of domain problems. Existing methods mainly depend on feature scoring functions or sparse regularizations; nonetheless, they have limited ability to reconcile the representativeness and inter-correlations of features. In this paper, we introduce a novel, simple yet effective regularization approach, named top-$k$ regularization, to supervised feature selection in regression and classification tasks. Structurally, the top-$k$ regularization induces a sub-architecture on the architecture of a learning model to boost its ability to select the most informative features and model complex nonlinear relationships simultaneously. Theoretically, we derive and mathematically prove a uniform approximation error bound for using this approach to approximate high-dimensional sparse functions. Extensive experiments on a wide variety of benchmarking datasets show that the top-$k$ regularization is effective and stable for supervised feature selection.

Yang Liu, Qian Zhang, Yongyong Chen et al.

It is a challenging task to remove heavy and mixed types of noise from Hyperspectral images (HSIs). In this paper, we propose a novel nonconvex approach to RPCA for HSI denoising, which adopts the log-determinant rank approximation and a novel $\ell_{2,\log}$ norm, to restrict the low-rank or column-wise sparse properties for the component matrices, respectively.For the $\ell_{2,\log}$-regularized shrinkage problem, we develop an efficient, closed-form solution, which is named $\ell_{2,\log}$-shrinkage operator, which can be generally used in other problems. Extensive experiments on both simulated and real HSIs demonstrate the effectiveness of the proposed method in denoising HSIs.

Xinxing Wu, Qiang Cheng

Graph neural networks have been used for a variety of learning tasks, such as link prediction, node classification, and node clustering. Among them, link prediction is a relatively under-studied graph learning task, with current state-of-the-art models based on one- or two-layer of shallow graph auto-encoder (GAE) architectures. In this paper, we focus on addressing a limitation of current methods for link prediction, which can only use shallow GAEs and variational GAEs, and creating effective methods to deepen (variational) GAE architectures to achieve stable and competitive performance. Our proposed methods innovatively incorporate standard auto-encoders (AEs) into the architectures of GAEs, where standard AEs are leveraged to learn essential, low-dimensional representations via seamlessly integrating the adjacency information and node features, while GAEs further build multi-scaled low-dimensional representations via residual connections to learn a compact overall embedding for link prediction. Empirically, extensive experiments on various benchmarking datasets verify the effectiveness of our methods and demonstrate the competitive performance of our deepened graph models for link prediction. Theoretically, we prove that our deep extensions inclusively express multiple polynomial filters with different orders.

Vasily Zadorozhnyy, Qiang Cheng, Qiang Ye

Generative adversarial network (GAN) has become one of the most important neural network models for classical unsupervised machine learning. A variety of discriminator loss functions have been developed to train GAN's discriminators and they all have a common structure: a sum of real and fake losses that only depends on the actual and generated data respectively. One challenge associated with an equally weighted sum of two losses is that the training may benefit one loss but harm the other, which we show causes instability and mode collapse. In this paper, we introduce a new family of discriminator loss functions that adopts a weighted sum of real and fake parts, which we call adaptive weighted loss functions or aw-loss functions. Using the gradients of the real and fake parts of the loss, we can adaptively choose weights to train a discriminator in the direction that benefits the GAN's stability. Our method can be potentially applied to any discriminator model with a loss that is a sum of the real and fake parts. Experiments validated the effectiveness of our loss functions on an unconditional image generation task, improving the baseline results by a significant margin on CIFAR-10, STL-10, and CIFAR-100 datasets in Inception Scores and FID.

Chong Peng, Qian Zhang, Zhao Kang et al.

Subspace clustering methods have been widely studied recently. When the inputs are 2-dimensional (2D) data, existing subspace clustering methods usually convert them into vectors, which severely damages inherent structures and relationships from original data. In this paper, we propose a novel subspace clustering method for 2D data. It directly uses 2D data as inputs such that the learning of representations benefits from inherent structures and relationships of the data. It simultaneously seeks image projection and representation coefficients such that they mutually enhance each other and lead to powerful data representations. An efficient algorithm is developed to solve the proposed objective function with provable decreasing and convergence property. Extensive experimental results verify the effectiveness of the new method.

Xinxing Wu, Qiang Cheng

Feature selection reduces the dimensionality of data by identifying a subset of the most informative features. In this paper, we propose an innovative framework for unsupervised feature selection, called fractal autoencoders (FAE). It trains a neural network to pinpoint informative features for global exploring of representability and for local excavating of diversity. Architecturally, FAE extends autoencoders by adding a one-to-one scoring layer and a small sub-neural network for feature selection in an unsupervised fashion. With such a concise architecture, FAE achieves state-of-the-art performances; extensive experimental results on fourteen datasets, including very high-dimensional data, have demonstrated the superiority of FAE over existing contemporary methods for unsupervised feature selection. In particular, FAE exhibits substantial advantages on gene expression data exploration, reducing measurement cost by about $15$\% over the widely used L1000 landmark genes. Further, we show that the FAE framework is easily extensible with an application.

Xinxing Wu, Qiang Cheng

Feature selection, as a vital dimension reduction technique, reduces data dimension by identifying an essential subset of input features, which can facilitate interpretable insights into learning and inference processes. Algorithmic stability is a key characteristic of an algorithm regarding its sensitivity to perturbations of input samples. In this paper, we propose an innovative unsupervised feature selection algorithm attaining this stability with provable guarantees. The architecture of our algorithm consists of a feature scorer and a feature selector. The scorer trains a neural network (NN) to globally score all the features, and the selector adopts a dependent sub-NN to locally evaluate the representation abilities for selecting features. Further, we present algorithmic stability analysis and show that our algorithm has a performance guarantee via a generalization error bound. Extensive experimental results on real-world datasets demonstrate superior generalization performance of our proposed algorithm to strong baseline methods. Also, the properties revealed by our theoretical analysis and the stability of our algorithm-selected features are empirically confirmed.

Zhao Kang, Chong Peng, Qiang Cheng et al.

Graphs have become increasingly popular in modeling structures and interactions in a wide variety of problems during the last decade. Graph-based clustering and semi-supervised classification techniques have shown impressive performance. This paper proposes a graph learning framework to preserve both the local and global structure of data. Specifically, our method uses the self-expressiveness of samples to capture the global structure and adaptive neighbor approach to respect the local structure. Furthermore, most existing graph-based methods conduct clustering and semi-supervised classification on the graph learned from the original data matrix, which doesn't have explicit cluster structure, thus they might not achieve the optimal performance. By considering rank constraint, the achieved graph will have exactly $c$ connected components if there are $c$ clusters or classes. As a byproduct of this, graph learning and label inference are jointly and iteratively implemented in a principled way. Theoretically, we show that our model is equivalent to a combination of kernel k-means and k-means methods under certain condition. Extensive experiments on clustering and semi-supervised classification demonstrate that the proposed method outperforms other state-of-the-art methods.

Chong Peng, Zhilu Zhang, Zhao Kang et al.

In this paper, we propose a new Semi-Nonnegative Matrix Factorization method for 2-dimensional (2D) data, named TS-NMF. It overcomes the drawback of existing methods that seriously damage the spatial information of the data by converting 2D data to vectors in a preprocessing step. In particular, projection matrices are sought under the guidance of building new data representations, such that the spatial information is retained and projections are enhanced by the goal of clustering, which helps construct optimal projection directions. Moreover, to exploit nonlinear structures of the data, manifold is constructed in the projected subspace, which is adaptively updated according to the projections and less afflicted with noise and outliers of the data and thus more representative in the projected space. Hence, seeking projections, building new data representations, and learning manifold are seamlessly integrated in a single model, which mutually enhance other and lead to a powerful data representation. Comprehensive experimental results verify the effectiveness of TS-NMF in comparison with several state-of-the-art algorithms, which suggests high potential of the proposed method for real world applications.

Chong Peng, Zhao Kang, Chenglizhao Chen et al.

Existing nonnegative matrix factorization methods focus on learning global structure of the data to construct basis and coefficient matrices, which ignores the local structure that commonly exists among data. In this paper, we propose a new type of nonnegative matrix factorization method, which learns local similarity and clustering in a mutually enhancing way. The learned new representation is more representative in that it better reveals inherent geometric property of the data. Nonlinear expansion is given and efficient multiplicative updates are developed with theoretical convergence guarantees. Extensive experimental results have confirmed the effectiveness of the proposed model.

Xinghua Yao, Qiang Cheng, Guo-Qiang Zhang

In current clinical practice, electroencephalograms (EEG) are reviewed and analyzed by well-trained neurologists to provide supports for therapeutic decisions. The way of manual reviewing is labor-intensive and error prone. Automatic and accurate seizure/nonseizure classification methods are needed. One major problem is that the EEG signals for seizure state and nonseizure state exhibit considerable variations. In order to capture essential seizure features, this paper integrates an emerging deep learning model, the independently recurrent neural network (IndRNN), with a dense structure and an attention mechanism to exploit temporal and spatial discriminating features and overcome seizure variabilities. The dense structure is to ensure maximum information flow between layers. The attention mechanism is to capture spatial features. Evaluations are performed in cross-validation experiments over the noisy CHB-MIT data set. The obtained average sensitivity, specificity and precision of 88.80%, 88.60% and 88.69% are better than using the current state-of-the-art methods. In addition, we explore how the segment length affects the classification performance. Thirteen different segment lengths are assessed, showing that the classification performance varies over the segment lengths, and the maximal fluctuating margin is more than 4%. Thus, the segment length is an important factor influencing the classification performance.

Chong Peng, Chenglizhao Chen, Zhao Kang et al.

Robust principal component analysis (RPCA) has drawn significant attentions due to its powerful capability in recovering low-rank matrices as well as successful appplications in various real world problems. The current state-of-the-art algorithms usually need to solve singular value decomposition of large matrices, which generally has at least a quadratic or even cubic complexity. This drawback has limited the application of RPCA in solving real world problems. To combat this drawback, in this paper we propose a new type of RPCA method, RES-PCA, which is linearly efficient and scalable in both data size and dimension. For comparison purpose, AltProj, an existing scalable approach to RPCA requires the precise knowlwdge of the true rank; otherwise, it may fail to recover low-rank matrices. By contrast, our method works with or without knowing the true rank; even when both methods work, our method is faster. Extensive experiments have been performed and testified to the effectiveness of proposed method quantitatively and in visual quality, which suggests that our method is suitable to be employed as a light-weight, scalable component for RPCA in any application pipelines.

Chong Peng, Qiang Cheng

We introduce a discriminative regression approach to supervised classification in this paper. It estimates a representation model while accounting for discriminativeness between classes, thereby enabling accurate derivation of categorical information. This new type of regression models extends existing models such as ridge, lasso, and group lasso through explicitly incorporating discriminative information. As a special case we focus on a quadratic model that admits a closed-form analytical solution. The corresponding classifier is called discriminative regression machine (DRM). Three iterative algorithms are further established for the DRM to enhance the efficiency and scalability for real applications. Our approach and the algorithms are applicable to general types of data including images, high-dimensional data, and imbalanced data. We compare the DRM with currently state-of-the-art classifiers. Our extensive experimental results show superior performance of the DRM and confirm the effectiveness of the proposed approach.

Xinghua Yao, Qiang Cheng, Guo-Qiang Zhang

In current clinical practices, electroencephalograms (EEG) are reviewed and analyzed by trained neurologists to provide supports for therapeutic decisions. Manual reviews can be laborious and error prone. Automatic and accurate seizure/non-seizure classification methods are desirable. A critical challenge is that seizure morphologies exhibit considerable variabilities. In order to capture essential seizure features, this paper leverages an emerging deep learning model, the independently recurrent neural network (IndRNN), to construct a new approach for the seizure/non-seizure classification. This new approach gradually expands the time scales, thereby extracting temporal and spatial features from the local time duration to the entire record. Evaluations are conducted with cross-validation experiments across subjects over the noisy data of CHB-MIT. Experimental results demonstrate that the proposed approach outperforms the current state-of-the-art methods. In addition, we explore how the segment length affects the classification performance. Thirteen different segment lengths are assessed, showing that the classification performance varies over the segment lengths, and the maximal fluctuating margin is more than 4%. Thus, the segment length is an important factor influencing the classification performance.

Liyu Gong, Qiang Cheng

In this paper, we propose an auto-encoder based generative neural network model whose encoder compresses the inputs into vectors in the tangent space of a special Lie group manifold: upper triangular positive definite affine transform matrices (UTDATs). UTDATs are representations of Gaussian distributions and can straightforwardly generate Gaussian distributed samples. Therefore, the encoder is trained together with a decoder (generator) which takes Gaussian distributed latent vectors as input. Compared with related generative models such as variational auto-encoder, the proposed model incorporates the information on geometric properties of Gaussian distributions. As a special case, we derive an exponential mapping layer for diagonal Gaussian UTDATs which eliminates matrix exponential operator compared with general exponential mapping in Lie group theory. Moreover, we derive an intrinsic loss for UTDAT Lie group which can be calculated as l-2 loss in the tangent space. Furthermore, inspired by the Lie group theory, we propose to use the Lie algebra vectors rather than the raw parameters (e.g. mean) of Gaussian distributions as compressed representations of original inputs. Experimental results verity the effectiveness of the proposed new generative model and the benefits gained from the Lie group structural information of UTDATs.

Liyu Gong, Qiang Cheng

Edge features contain important information about graphs. However, current state-of-the-art neural network models designed for graph learning, e.g. graph convolutional networks (GCN) and graph attention networks (GAT), adequately utilize edge features, especially multi-dimensional edge features. In this paper, we build a new framework for a family of new graph neural network models that can more sufficiently exploit edge features, including those of undirected or multi-dimensional edges. The proposed framework can consolidate current graph neural network models; e.g. graph convolutional networks (GCN) and graph attention networks (GAT). The proposed framework and new models have the following novelties: First, we propose to use doubly stochastic normalization of graph edge features instead of the commonly used row or symmetric normalization approches used in current graph neural networks. Second, we construct new formulas for the operations in each individual layer so that they can handle multi-dimensional edge features. Third, for the proposed new framework, edge features are adaptive across network layers. As a result, our proposed new framework and new models can exploit a rich source of graph information. We apply our new models to graph node classification on several citation networks, whole graph classification, and regression on several molecular datasets. Compared with the current state-of-the-art methods, i.e. GCNs and GAT, our models obtain better performance, which testify to the importance of exploiting edge features in graph neural networks.

Zhao Kang, Chong Peng, Qiang Cheng et al.

Spectral clustering has found extensive use in many areas. Most traditional spectral clustering algorithms work in three separate steps: similarity graph construction; continuous labels learning; discretizing the learned labels by k-means clustering. Such common practice has two potential flaws, which may lead to severe information loss and performance degradation. First, predefined similarity graph might not be optimal for subsequent clustering. It is well-accepted that similarity graph highly affects the clustering results. To this end, we propose to automatically learn similarity information from data and simultaneously consider the constraint that the similarity matrix has exact c connected components if there are c clusters. Second, the discrete solution may deviate from the spectral solution since k-means method is well-known as sensitive to the initialization of cluster centers. In this work, we transform the candidate solution into a new one that better approximates the discrete one. Finally, those three subtasks are integrated into a unified framework, with each subtask iteratively boosted by using the results of the others towards an overall optimal solution. It is known that the performance of a kernel method is largely determined by the choice of kernels. To tackle this practical problem of how to select the most suitable kernel for a particular data set, we further extend our model to incorporate multiple kernel learning ability. Extensive experiments demonstrate the superiority of our proposed method as compared to existing clustering approaches.

Zhao Kang, Chong Peng, Qiang Cheng

Many similarity-based clustering methods work in two separate steps including similarity matrix computation and subsequent spectral clustering. However, similarity measurement is challenging because it is usually impacted by many factors, e.g., the choice of similarity metric, neighborhood size, scale of data, noise and outliers. Thus the learned similarity matrix is often not suitable, let alone optimal, for the subsequent clustering. In addition, nonlinear similarity often exists in many real world data which, however, has not been effectively considered by most existing methods. To tackle these two challenges, we propose a model to simultaneously learn cluster indicator matrix and similarity information in kernel spaces in a principled way. We show theoretical relationships to kernel k-means, k-means, and spectral clustering methods. Then, to address the practical issue of how to select the most suitable kernel for a particular clustering task, we further extend our model with a multiple kernel learning ability. With this joint model, we can automatically accomplish three subtasks of finding the best cluster indicator matrix, the most accurate similarity relations and the optimal combination of multiple kernels. By leveraging the interactions between these three subtasks in a joint framework, each subtask can be iteratively boosted by using the results of the others towards an overall optimal solution. Extensive experiments are performed to demonstrate the effectiveness of our method.

Zhao Kang, Chong Peng, Ming Yang et al.

Recommender systems play an increasingly important role in online applications to help users find what they need or prefer. Collaborative filtering algorithms that generate predictions by analyzing the user-item rating matrix perform poorly when the matrix is sparse. To alleviate this problem, this paper proposes a simple recommendation algorithm that fully exploits the similarity information among users and items and intrinsic structural information of the user-item matrix. The proposed method constructs a new representation which preserves affinity and structure information in the user-item rating matrix and then performs recommendation task. To capture proximity information about users and items, two graphs are constructed. Manifold learning idea is used to constrain the new representation to be smooth on these graphs, so as to enforce users and item proximities. Our model is formulated as a convex optimization problem, for which we need to solve the well-known Sylvester equation only. We carry out extensive empirical evaluations on six benchmark datasets to show the effectiveness of this approach.

Zhao Kang, Qiang Cheng

The importance of accurate recommender systems has been widely recognized by academia and industry. However, the recommendation quality is still rather low. Recently, a linear sparse and low-rank representation of the user-item matrix has been applied to produce Top-N recommendations. This approach uses the nuclear norm as a convex relaxation for the rank function and has achieved better recommendation accuracy than the state-of-the-art methods. In the past several years, solving rank minimization problems by leveraging nonconvex relaxations has received increasing attention. Some empirical results demonstrate that it can provide a better approximation to original problems than convex relaxation. In this paper, we propose a novel rank approximation to enhance the performance of Top-N recommendation systems, where the approximation error is controllable. Experimental results on real data show that the proposed rank approximation improves the Top-$N$ recommendation accuracy substantially.

Zhao Kang, Chong Peng, Qiang Cheng

Top-N recommender systems have been investigated widely both in industry and academia. However, the recommendation quality is far from satisfactory. In this paper, we propose a simple yet promising algorithm. We fill the user-item matrix based on a low-rank assumption and simultaneously keep the original information. To do that, a nonconvex rank relaxation rather than the nuclear norm is adopted to provide a better rank approximation and an efficient optimization strategy is designed. A comprehensive set of experiments on real datasets demonstrates that our method pushes the accuracy of Top-N recommendation to a new level.

Zhao Kang, Chong Peng, Qiang Cheng

Numerous applications in data mining and machine learning require recovering a matrix of minimal rank. Robust principal component analysis (RPCA) is a general framework for handling this kind of problems. Nuclear norm based convex surrogate of the rank function in RPCA is widely investigated. Under certain assumptions, it can recover the underlying true low rank matrix with high probability. However, those assumptions may not hold in real-world applications. Since the nuclear norm approximates the rank by adding all singular values together, which is essentially a $\ell_1$-norm of the singular values, the resulting approximation error is not trivial and thus the resulting matrix estimator can be significantly biased. To seek a closer approximation and to alleviate the above-mentioned limitations of the nuclear norm, we propose a nonconvex rank approximation. This approximation to the matrix rank is tighter than the nuclear norm. To solve the associated nonconvex minimization problem, we develop an efficient augmented Lagrange multiplier based optimization algorithm. Experimental results demonstrate that our method outperforms current state-of-the-art algorithms in both accuracy and efficiency.

Zhao Kang, Chong Peng, Qiang Cheng

Matrix rank minimization problem is in general NP-hard. The nuclear norm is used to substitute the rank function in many recent studies. Nevertheless, the nuclear norm approximation adds all singular values together and the approximation error may depend heavily on the magnitudes of singular values. This might restrict its capability in dealing with many practical problems. In this paper, an arctangent function is used as a tighter approximation to the rank function. We use it on the challenging subspace clustering problem. For this nonconvex minimization problem, we develop an effective optimization procedure based on a type of augmented Lagrange multipliers (ALM) method. Extensive experiments on face clustering and motion segmentation show that the proposed method is effective for rank approximation.