Exploring structure diversity in atomic resolution microscopy with graph neural networks

The emergence of deep learning (DL) has provided great opportunities for the high-throughput analysis of atomic-resolution micrographs. However, the DL models trained by image patches in fixed size generally lack efficiency and flexibility when processing micrographs containing diversified atomic configurations. Herein, inspired by the similarity between the atomic structures and graphs, we describe a few-shot learning framework based on an equivariant graph neural network (EGNN) to analyze a library of atomic structures (e.g., vacancies, phases, grain boundaries, doping, etc.), showing significantly promoted robustness and three orders of magnitude reduced computing parameters compared to the image-driven DL models, which is especially evident for those aggregated vacancy lines with flexible lattice distortion. Besides, the intuitiveness of graphs enables quantitative and straightforward extraction of the atomic-scale structural features in batches, thus statistically unveiling the self-assembly dynamics of vacancy lines under electron beam irradiation. A versatile model toolkit is established by integrating EGNN sub-models for single structure recognition to process images involving varied configurations in the form of a task chain, leading to the discovery of novel doping configurations with superior electrocatalytic properties for hydrogen evolution reactions. This work provides a powerful tool to explore structure diversity in a fast, accurate, and intelligent manner.

H2OVL-Mississippi Vision Language Models Technical Report

Smaller vision-language models (VLMs) are becoming increasingly important for privacy-focused, on-device applications due to their ability to run efficiently on consumer hardware for processing enterprise commercial documents and images. These models require strong language understanding and visual capabilities to enhance human-machine interaction. To address this need, we present H2OVL-Mississippi, a pair of small VLMs trained on 37 million image-text pairs using 240 hours of compute on 8 x H100 GPUs. H2OVL-Mississippi-0.8B is a tiny model with 0.8 billion parameters that specializes in text recognition, achieving state of the art performance on the Text Recognition portion of OCRBench and surpassing much larger models in this area. Additionally, we are releasing H2OVL-Mississippi-2B, a 2 billion parameter model for general use cases, exhibiting highly competitive metrics across various academic benchmarks. Both models build upon our prior work with H2O-Danube language models, extending their capabilities into the visual domain. We release them under the Apache 2.0 license, making VLMs accessible to everyone, democratizing document AI and visual LLMs.

MGSA: Multi-granularity Graph Structure Attention for Knowledge Graph-to-Text Generation

The Knowledge Graph-to-Text Generation task aims to convert structured knowledge graphs into coherent and human-readable natural language text. Recent efforts in this field have focused on enhancing pre-trained language models (PLMs) by incorporating graph structure information to capture the intricate structure details of knowledge graphs. However, most of these approaches tend to capture only single-granularity structure information, concentrating either on the relationships between entities within the original graph or on the relationships between words within the same entity or across different entities. This narrow focus results in a significant limitation: models that concentrate solely on entity-level structure fail to capture the nuanced semantic relationships between words, while those that focus only on word-level structure overlook the broader relationships between original entire entities. To overcome these limitations, this paper introduces the Multi-granularity Graph Structure Attention (MGSA), which is based on PLMs. The encoder of the model architecture features an entity-level structure encoding module, a word-level structure encoding module, and an aggregation module that synthesizes information from both structure. This multi-granularity structure encoding approach allows the model to simultaneously capture both entity-level and word-level structure information, providing a more comprehensive understanding of the knowledge graph's structure information, thereby significantly improving the quality of the generated text. We conducted extensive evaluations of the MGSA model using two widely recognized KG-to-Text Generation benchmark datasets, WebNLG and EventNarrative, where it consistently outperformed models that rely solely on single-granularity structure information, demonstrating the effectiveness of our approach.

Dual-stream Feature Augmentation for Domain Generalization

Domain generalization (DG) task aims to learn a robust model from source domains that could handle the out-of-distribution (OOD) issue. In order to improve the generalization ability of the model in unseen domains, increasing the diversity of training samples is an effective solution. However, existing augmentation approaches always have some limitations. On the one hand, the augmentation manner in most DG methods is not enough as the model may not see the perturbed features in approximate the worst case due to the randomness, thus the transferability in features could not be fully explored. On the other hand, the causality in discriminative features is not involved in these methods, which harms the generalization ability of model due to the spurious correlations. To address these issues, we propose a Dual-stream Feature Augmentation~(DFA) method by constructing some hard features from two perspectives. Firstly, to improve the transferability, we construct some targeted features with domain related augmentation manner. Through the guidance of uncertainty, some hard cross-domain fictitious features are generated to simulate domain shift. Secondly, to take the causality into consideration, the spurious correlated non-causal information is disentangled by an adversarial mask, then the more discriminative features can be extracted through these hard causal related information. Different from previous fixed synthesizing strategy, the two augmentations are integrated into a unified learnable feature disentangle model. Based on these hard features, contrastive learning is employed to keep the semantic consistency and improve the robustness of the model. Extensive experiments on several datasets demonstrated that our approach could achieve state-of-the-art performance for domain generalization. Our code is available at: https://github.com/alusi123/DFA.

RobNODDI: Robust NODDI Parameter Estimation with Adaptive Sampling under Continuous Representation

Neurite Orientation Dispersion and Density Imaging (NODDI) is an important imaging technology used to evaluate the microstructure of brain tissue, which is of great significance for the discovery and treatment of various neurological diseases. Current deep learning-based methods perform parameter estimation through diffusion magnetic resonance imaging (dMRI) with a small number of diffusion gradients. These methods speed up parameter estimation and improve accuracy. However, the diffusion directions used by most existing deep learning models during testing needs to be strictly consistent with the diffusion directions during training. This results in poor generalization and robustness of deep learning models in dMRI parameter estimation. In this work, we verify for the first time that the parameter estimation performance of current mainstream methods will significantly decrease when the testing diffusion directions and the training diffusion directions are inconsistent. A robust NODDI parameter estimation method with adaptive sampling under continuous representation (RobNODDI) is proposed. Furthermore, long short-term memory (LSTM) units and fully connected layers are selected to learn continuous representation signals. To this end, we use a total of 100 subjects to conduct experiments based on the Human Connectome Project (HCP) dataset, of which 60 are used for training, 20 are used for validation, and 20 are used for testing. The test results indicate that RobNODDI improves the generalization performance and robustness of the deep learning model, enhancing the stability and flexibility of deep learning NODDI parameter estimatimation applications.

Gradually Vanishing Gap in Prototypical Network for Unsupervised Domain Adaptation

Unsupervised domain adaptation (UDA) is a critical problem for transfer learning, which aims to transfer the semantic information from labeled source domain to unlabeled target domain. Recent advancements in UDA models have demonstrated significant generalization capabilities on the target domain. However, the generalization boundary of UDA models remains unclear. When the domain discrepancy is too large, the model can not preserve the distribution structure, leading to distribution collapse during the alignment. To address this challenge, we propose an efficient UDA framework named Gradually Vanishing Gap in Prototypical Network (GVG-PN), which achieves transfer learning from both global and local perspectives. From the global alignment standpoint, our model generates a domain-biased intermediate domain that helps preserve the distribution structures. By entangling cross-domain features, our model progressively reduces the risk of distribution collapse. However, only relying on global alignment is insufficient to preserve the distribution structure. To further enhance the inner relationships of features, we introduce the local perspective. We utilize the graph convolutional network (GCN) as an intuitive method to explore the internal relationships between features, ensuring the preservation of manifold structures and generating domain-biased prototypes. Additionally, we consider the discriminability of the inner relationships between features. We propose a pro-contrastive loss to enhance the discriminability at the prototype level by separating hard negative pairs. By incorporating both GCN and the pro-contrastive loss, our model fully explores fine-grained semantic relationships. Experiments on several UDA benchmarks validated that the proposed GVG-PN can clearly outperform the SOTA models.

Dual-State Personalized Knowledge Tracing with Emotional Incorporation

Knowledge tracing has been widely used in online learning systems to guide the students' future learning. However, most existing KT models primarily focus on extracting abundant information from the question sets and explore the relationships between them, but ignore the personalized student behavioral information in the learning process. This will limit the model's ability to accurately capture the personalized knowledge states of students and reasonably predict their performances. To alleviate this limitation, we explicitly models the personalized learning process by incorporating the emotions, a representative personalized behavior in the learning process, into KT framework. Specifically, we present a novel Dual-State Personalized Knowledge Tracing with Emotional Incorporation model to achieve this goal: Firstly, we incorporate emotional information into the modeling process of knowledge state, resulting in the Knowledge State Boosting Module. Secondly, we design an Emotional State Tracing Module to monitor students' personalized emotional states, and propose an emotion prediction method based on personalized emotional states. Finally, we apply the predicted emotions to enhance students' response prediction. Furthermore, to extend the generalization capability of our model across different datasets, we design a transferred version of DEKT, named Transfer Learning-based Self-loop model (T-DEKT). Extensive experiments show our method achieves the state-of-the-art performance.

DeepMpMRI: Tensor-decomposition Regularized Learning for Fast and High-Fidelity Multi-Parametric Microstructural MR Imaging

Deep learning has emerged as a promising approach for learning the nonlinear mapping between diffusion-weighted MR images and tissue parameters, which enables automatic and deep understanding of the brain microstructures. However, the efficiency and accuracy in the multi-parametric estimations are still limited since previous studies tend to estimate multi-parametric maps with dense sampling and isolated signal modeling. This paper proposes DeepMpMRI, a unified framework for fast and high-fidelity multi-parametric estimation from various diffusion models using sparsely sampled q-space data. DeepMpMRI is equipped with a newly designed tensor-decomposition-based regularizer to effectively capture fine details by exploiting the correlation across parameters. In addition, we introduce a Nesterov-based adaptive learning algorithm that optimizes the regularization parameter dynamically to enhance the performance. DeepMpMRI is an extendable framework capable of incorporating flexible network architecture. Experimental results demonstrate the superiority of our approach over 5 state-of-the-art methods in simultaneously estimating multi-parametric maps for various diffusion models with fine-grained details both quantitatively and qualitatively, achieving 4.5 - 22.5$\times$ acceleration compared to the dense sampling of a total of 270 diffusion gradients.

Personalized Forgetting Mechanism with Concept-Driven Knowledge Tracing

Knowledge Tracing (KT) aims to trace changes in students' knowledge states throughout their entire learning process by analyzing their historical learning data and predicting their future learning performance. Existing forgetting curve theory based knowledge tracing models only consider the general forgetting caused by time intervals, ignoring the individualization of students and the causal relationship of the forgetting process. To address these problems, we propose a Concept-driven Personalized Forgetting knowledge tracing model (CPF) which integrates hierarchical relationships between knowledge concepts and incorporates students' personalized cognitive abilities. First, we integrate the students' personalized capabilities into both the learning and forgetting processes to explicitly distinguish students' individual learning gains and forgetting rates according to their cognitive abilities. Second, we take into account the hierarchical relationships between knowledge points and design a precursor-successor knowledge concept matrix to simulate the causal relationship in the forgetting process, while also integrating the potential impact of forgetting prior knowledge points on subsequent ones. The proposed personalized forgetting mechanism can not only be applied to the learning of specifc knowledge concepts but also the life-long learning process. Extensive experimental results on three public datasets show that our CPF outperforms current forgetting curve theory based methods in predicting student performance, demonstrating CPF can better simulate changes in students' knowledge status through the personalized forgetting mechanism.

CSR-dMRI: Continuous Super-Resolution of Diffusion MRI with Anatomical Structure-assisted Implicit Neural Representation Learning

Deep learning-based dMRI super-resolution methods can effectively enhance image resolution by leveraging the learning capabilities of neural networks on large datasets. However, these methods tend to learn a fixed scale mapping between low-resolution (LR) and high-resolution (HR) images, overlooking the need for radiologists to scale the images at arbitrary resolutions. Moreover, the pixel-wise loss in the image domain tends to generate over-smoothed results, losing fine textures and edge information. To address these issues, we propose a novel continuous super-resolution of dMRI with anatomical structure-assisted implicit neural representation learning method, called CSR-dMRI. Specifically, the CSR-dMRI model consists of two components. The first is the latent feature extractor, which primarily extracts latent space feature maps from LR dMRI and anatomical images while learning structural prior information from the anatomical images. The second is the implicit function network, which utilizes voxel coordinates and latent feature vectors to generate voxel intensities at corresponding positions. Additionally, a frequency-domain-based loss is introduced to preserve the structural and texture information, further enhancing the image quality. Extensive experiments on the publicly available HCP dataset validate the effectiveness of our approach. Furthermore, our method demonstrates superior generalization capability and can be applied to arbitrary-scale super-resolution, including non-integer scale factors, expanding its applicability beyond conventional approaches.