Probability Distribution Alignment and Low-Rank Weight Decomposition for Source-Free Domain Adaptive Brain Decoding

Brain decoding currently faces significant challenges in individual differences, modality alignment, and high-dimensional embeddings. To address individual differences, researchers often use source subject data, which leads to issues such as privacy leakage and heavy data storage burdens. In modality alignment, current works focus on aligning the softmax probability distribution but neglect the alignment of marginal probability distributions, resulting in modality misalignment. Additionally, images and text are aligned separately with fMRI without considering the complex interplay between images and text, leading to poor image reconstruction. Finally, the enormous dimensionality of CLIP embeddings causes significant computational costs. Although the dimensionality of CLIP embeddings can be reduced by ignoring the number of patches obtained from images and the number of tokens acquired from text, this comes at the cost of a significant drop in model performance, creating a dilemma. To overcome these limitations, we propose a source-free domain adaptation-based brain decoding framework.

Artifact detection and localization in single-channel mobile EEG for sleep research using deep learning and attention mechanisms

Artifacts in the electroencephalogram (EEG) degrade signal quality and impact the analysis of brain activity. Current methods for detecting artifacts in sleep EEG rely on simple threshold-based algorithms that require manual intervention, which is time-consuming and impractical due to the vast volume of data that novel mobile recording systems generate. We propose a convolutional neural network (CNN) model incorporating a convolutional block attention module (CNN-CBAM) to detect and identify the location of artifacts in the sleep EEG with attention maps. We benchmarked this model against six other machine learning and signal processing approaches. We trained/tuned all models on 72 manually annotated EEG recordings obtained during home-based monitoring from 18 healthy participants with a mean (SD) age of 68.05 y ($\pm$5.02). We tested them on 26 separate recordings from 6 healthy participants with a mean (SD) age of 68.33 y ($\pm$4.08), with contained artifacts in 4\% of epochs. CNN-CBAM achieved the highest area under the receiver operating characteristic curve (0.88), sensitivity (0.81), and specificity (0.86) when compared to the other approaches. The attention maps from CNN-CBAM localized artifacts within the epoch with a sensitivity of 0.71 and specificity of 0.67. This work demonstrates the feasibility of automating the detection and localization of artifacts in wearable sleep EEG.

mmHRR: Monitoring Heart Rate Recovery with Millimeter Wave Radar

Heart rate recovery (HRR) within the initial minute following exercise is a widely utilized metric for assessing cardiac autonomic function in individuals and predicting mortality risk in patients with cardiovascular disease. However, prevailing solutions for HRR monitoring typically involve the use of specialized medical equipment or contact wearable sensors, resulting in high costs and poor user experience. In this paper, we propose a contactless HRR monitoring technique, mmHRR, which achieves accurate heart rate (HR) estimation with a commercial mmWave radar. Unlike HR estimation at rest, the HR varies quickly after exercise and the heartbeat signal entangles with the respiration harmonics. To overcome these hurdles and effectively estimate the HR from the weak and non-stationary heartbeat signal, we propose a novel signal processing pipeline, including dynamic target tracking, adaptive heartbeat signal extraction, and accurate HR estimation with composite sliding windows. Real-world experiments demonstrate that mmHRR exhibits exceptional robustness across diverse environmental conditions, and achieves an average HR estimation error of 3.31 bpm (beats per minute), 71% lower than that of the state-of-the-art method.

D3: Diversity, Difficulty, and Dependability-Aware Data Selection for Sample-Efficient LLM Instruction Tuning

Recent advancements in instruction tuning for large language models (LLMs) suggest that a small, high-quality dataset can significantly equip LLMs with instruction-following capabilities, outperforming large datasets often burdened by quality and redundancy issues. However, the challenge lies in automatically identifying valuable subsets from large datasets to boost both the effectiveness and efficiency of instruction tuning. In this paper, we first establish data selection criteria based on three distinct aspects of data value: diversity, difficulty, and dependability, and then propose the D3 method comprising two key steps of scoring and selection. Specifically, in the scoring step, we define the diversity function to measure sample distinctiveness and introduce the uncertainty-based prediction difficulty to evaluate sample difficulty by mitigating the interference of context-oriented generation diversity. Additionally, we integrate an external LLM for dependability assessment. In the selection step, we formulate the D3 weighted coreset objective, which jointly optimizes three aspects of data value to solve for the most valuable subset. The two steps of D3 can iterate multiple rounds, incorporating feedback to refine the selection focus adaptively. Experiments on three datasets demonstrate the effectiveness of D3 in endowing LLMs with competitive or even superior instruction-following capabilities using less than 10% of the entire dataset.

UniGenX: Unified Generation of Sequence and Structure with Autoregressive Diffusion

Unified generation of sequence and structure for scientific data (e.g., materials, molecules, proteins) is a critical task. Existing approaches primarily rely on either autoregressive sequence models or diffusion models, each offering distinct advantages and facing notable limitations. Autoregressive models, such as GPT, Llama, and Phi-4, have demonstrated remarkable success in natural language generation and have been extended to multimodal tasks (e.g., image, video, and audio) using advanced encoders like VQ-VAE to represent complex modalities as discrete sequences. However, their direct application to scientific domains is challenging due to the high precision requirements and the diverse nature of scientific data. On the other hand, diffusion models excel at generating high-dimensional scientific data, such as protein, molecule, and material structures, with remarkable accuracy. Yet, their inability to effectively model sequences limits their potential as general-purpose multimodal foundation models. To address these challenges, we propose UniGenX, a unified framework that combines autoregressive next-token prediction with conditional diffusion models. This integration leverages the strengths of autoregressive models to ease the training of conditional diffusion models, while diffusion-based generative heads enhance the precision of autoregressive predictions. We validate the effectiveness of UniGenX on material and small molecule generation tasks, achieving a significant leap in state-of-the-art performance for material crystal structure prediction and establishing new state-of-the-art results for small molecule structure prediction, de novo design, and conditional generation. Notably, UniGenX demonstrates significant improvements, especially in handling long sequences for complex structures, showcasing its efficacy as a versatile tool for scientific data generation.

X-GAN: A Generative AI-Powered Unsupervised Model for High-Precision Segmentation of Retinal Main Vessels toward Early Detection of Glaucoma

Structural changes in main retinal blood vessels serve as critical biomarkers for the onset and progression of glaucoma. Identifying these vessels is vital for vascular modeling yet highly challenging. This paper proposes X-GAN, a generative AI-powered unsupervised segmentation model designed for extracting main blood vessels from Optical Coherence Tomography Angiography (OCTA) images. The process begins with the Space Colonization Algorithm (SCA) to rapidly generate a skeleton of vessels, featuring their radii. By synergistically integrating generative adversarial networks (GANs) with biostatistical modeling of vessel radii, X-GAN enables a fast reconstruction of both 2D and 3D representations of the vessels. Based on this reconstruction, X-GAN achieves nearly 100\% segmentation accuracy without relying on labeled data or high-performance computing resources. Also, to address the Issue, data scarity, we introduce GSS-RetVein, a high-definition mixed 2D and 3D glaucoma retinal dataset. GSS-RetVein provides a rigorous benchmark due to its exceptionally clear capillary structures, introducing controlled noise for testing model robustness. Its 2D images feature sharp capillary boundaries, while its 3D component enhances vascular reconstruction and blood flow prediction, supporting glaucoma progression simulations. Experimental results confirm GSS-RetVein's superiority in evaluating main vessel segmentation compared to existing datasets. Code and dataset are here: https://github.com/VikiXie/SatMar8.

Enhancing the Scalability and Applicability of Kohn-Sham Hamiltonians for Molecular Systems

Density Functional Theory (DFT) is a pivotal method within quantum chemistry and materials science, with its core involving the construction and solution of the Kohn-Sham Hamiltonian. Despite its importance, the application of DFT is frequently limited by the substantial computational resources required to construct the Kohn-Sham Hamiltonian. In response to these limitations, current research has employed deep-learning models to efficiently predict molecular and solid Hamiltonians, with roto-translational symmetries encoded in their neural networks. However, the scalability of prior models may be problematic when applied to large molecules, resulting in non-physical predictions of ground-state properties. In this study, we generate a substantially larger training set (PubChemQH) than used previously and use it to create a scalable model for DFT calculations with physical accuracy. For our model, we introduce a loss function derived from physical principles, which we call Wavefunction Alignment Loss (WALoss). WALoss involves performing a basis change on the predicted Hamiltonian to align it with the observed one; thus, the resulting differences can serve as a surrogate for orbital energy differences, allowing models to make better predictions for molecular orbitals and total energies than previously possible. WALoss also substantially accelerates self-consistent-field (SCF) DFT calculations. Here, we show it achieves a reduction in total energy prediction error by a factor of 1347 and an SCF calculation speed-up by a factor of 18%. These substantial improvements set new benchmarks for achieving accurate and applicable predictions in larger molecular systems.

NatureLM: Deciphering the Language of Nature for Scientific Discovery

Foundation models have revolutionized natural language processing and artificial intelligence, significantly enhancing how machines comprehend and generate human languages. Inspired by the success of these foundation models, researchers have developed foundation models for individual scientific domains, including small molecules, materials, proteins, DNA, and RNA. However, these models are typically trained in isolation, lacking the ability to integrate across different scientific domains. Recognizing that entities within these domains can all be represented as sequences, which together form the "language of nature", we introduce Nature Language Model (briefly, NatureLM), a sequence-based science foundation model designed for scientific discovery. Pre-trained with data from multiple scientific domains, NatureLM offers a unified, versatile model that enables various applications including: (i) generating and optimizing small molecules, proteins, RNA, and materials using text instructions; (ii) cross-domain generation/design, such as protein-to-molecule and protein-to-RNA generation; and (iii) achieving state-of-the-art performance in tasks like SMILES-to-IUPAC translation and retrosynthesis on USPTO-50k. NatureLM offers a promising generalist approach for various scientific tasks, including drug discovery (hit generation/optimization, ADMET optimization, synthesis), novel material design, and the development of therapeutic proteins or nucleotides. We have developed NatureLM models in different sizes (1 billion, 8 billion, and 46.7 billion parameters) and observed a clear improvement in performance as the model size increases.

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

Hamiltonian matrix prediction is pivotal in computational chemistry, serving as the foundation for determining a wide range of molecular properties. While SE(3) equivariant graph neural networks have achieved remarkable success in this domain, their substantial computational cost-driven by high-order tensor product (TP) operations-restricts their scalability to large molecular systems with extensive basis sets. To address this challenge, we introduce SPHNet, an efficient and scalable equivariant network that incorporates adaptive sparsity into Hamiltonian prediction. SPHNet employs two innovative sparse gates to selectively constrain non-critical interaction combinations, significantly reducing tensor product computations while maintaining accuracy. To optimize the sparse representation, we develop a Three-phase Sparsity Scheduler, ensuring stable convergence and achieving high performance at sparsity rates of up to 70 percent. Extensive evaluations on QH9 and PubchemQH datasets demonstrate that SPHNet achieves state-of-the-art accuracy while providing up to a 7x speedup over existing models. Beyond Hamiltonian prediction, the proposed sparsification techniques also hold significant potential for improving the efficiency and scalability of other SE(3) equivariant networks, further broadening their applicability and impact.

\underline{E2}Former: A Linear-time \underline{E}fficient and \underline{E}quivariant Trans\underline{former} for Scalable Molecular Modeling

Equivariant Graph Neural Networks (EGNNs) have demonstrated significant success in modeling microscale systems, including those in chemistry, biology and materials science. However, EGNNs face substantial computational challenges due to the high cost of constructing edge features via spherical tensor products, making them impractical for large-scale systems. To address this limitation, we introduce E2Former, an equivariant and efficient transformer architecture that incorporates the Wigner $6j$ convolution (Wigner $6j$ Conv). By shifting the computational burden from edges to nodes, the Wigner $6j$ Conv reduces the complexity from $O(|\mathcal{E}|)$ to $ O(| \mathcal{V}|)$ while preserving both the model's expressive power and rotational equivariance. We show that this approach achieves a 7x-30x speedup compared to conventional $\mathrm{SO}(3)$ convolutions. Furthermore, our empirical results demonstrate that the derived E2Former mitigates the computational challenges of existing approaches without compromising the ability to capture detailed geometric information. This development could suggest a promising direction for scalable and efficient molecular modeling.