TabNSA: Native Sparse Attention for Efficient Tabular Data Learning

Tabular data poses unique challenges for deep learning due to its heterogeneous features and lack of inherent spatial structure. This paper introduces TabNSA, a novel deep learning architecture leveraging Native Sparse Attention (NSA) specifically for efficient tabular data processing. TabNSA incorporates a dynamic hierarchical sparse strategy, combining coarse-grained feature compression with fine-grained feature selection to preserve both global context awareness and local precision. By dynamically focusing on relevant subsets of features, TabNSA effectively captures intricate feature interactions. Extensive experiments demonstrate that TabNSA consistently outperforms existing methods, including both deep learning architectures and ensemble decision trees, achieving state-of-the-art performance across various benchmark datasets.

Mol-CADiff: Causality-Aware Autoregressive Diffusion for Molecule Generation

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.

CausalGeD: Blending Causality and Diffusion for Spatial Gene Expression Generation

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.

PROTECT: Protein circadian time prediction using unsupervised learning

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.

Deep Learning in Single-Cell and Spatial Transcriptomics Data Analysis: Advances and Challenges from a Data Science Perspective

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.

A physics-based perspective for understanding and utilizing spatial resources of wireless channels

To satisfy the increasing demands for transmission rates of wireless communications, it is necessary to use spatial resources of electromagnetic (EM) waves. In this context, EM information theory (EIT) has become a hot topic by integrating the theoretical framework of deterministic mathematics and stochastic statistics to explore the transmission mechanisms of continuous EM waves. However, the previous studies were primarily focused on frame analysis, with limited exploration of practical applications and a comprehensive understanding of its essential physical characteristics. In this paper, we present a three-dimensional (3-D) line-of-sight channel capacity formula that captures the vector EM physics and accommodates both near- and far-field scenes. Based on the rigorous mathematical equation and the physical mechanism of fast multipole expansion, a channel model is established, and the finite angular spectral bandwidth feature of scattered waves is revealed. To adapt to the feature of the channel, an optimization problem is formulated for determining the mode currents on the transmitter, aiming to obtain the optimal design of the precoder and combiner. We make comprehensive analyses to investigate the relationship among the spatial degree of freedom, noise, and transmitted power, thereby establishing a rigorous upper bound of channel capacity. A series of simulations are conducted to validate the theoretical model and numerical method. This work offers a novel perspective and methodology for understanding and leveraging EIT, and provides a theoretical foundation for the design and optimization of future wireless communications.

Comparative Analysis of Transfer Learning Models for Breast Cancer Classification

The classification of histopathological images is crucial for the early and precise detection of breast cancer. This study investigates the efficiency of deep learning models in distinguishing between Invasive Ductal Carcinoma (IDC) and non-IDC in histopathology slides. We conducted a thorough comparison examination of eight sophisticated models: ResNet-50, DenseNet-121, ResNeXt-50, Vision Transformer (ViT), GoogLeNet (Inception v3), EfficientNet, MobileNet, and SqueezeNet. This analysis was carried out using a large dataset of 277,524 image patches. Our research makes a substantial contribution to the field by offering a comprehensive assessment of the performance of each model. We particularly highlight the exceptional efficacy of attention-based mechanisms in the ViT model, which achieved a remarkable validation accuracy of 93\%, surpassing conventional convolutional networks. This study highlights the promise of advanced machine learning approaches in clinical settings, offering improved precision as well as efficiency in breast cancer diagnosis.

TSCMamba: Mamba Meets Multi-View Learning for Time Series Classification

Time series classification (TSC) on multivariate time series is a critical problem. We propose a novel multi-view approach integrating frequency-domain and time-domain features to provide complementary contexts for TSC. Our method fuses continuous wavelet transform spectral features with temporal convolutional or multilayer perceptron features. We leverage the Mamba state space model for efficient and scalable sequence modeling. We also introduce a novel tango scanning scheme to better model sequence relationships. Experiments on 10 standard benchmark datasets demonstrate our approach achieves an average 6.45% accuracy improvement over state-of-the-art TSC models.

TimeMachine: A Time Series is Worth 4 Mambas for Long-term Forecasting

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

MambaTab: A Simple Yet Effective Approach for Handling Tabular Data

Tabular data remains ubiquitous across domains despite growing use of images and texts for machine learning. While deep learning models like convolutional neural networks and transformers achieve strong performance on tabular data, they require extensive data preprocessing, tuning, and resources, limiting accessibility and scalability. This work develops 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 and minimal preprocessing, as empirically validated on diverse benchmark datasets. MambaTab's efficiency, scalability, generalizability, and predictive gains signify it as a lightweight, "out-of-the-box" solution for diverse tabular data with promise for enabling wider practical applications.