arXiv subjects

Mengjia Xu

Publications and source records attributed to Mengjia Xu.

At least 19 recordsLinked to original sources

arXiv2026

Multilevel Graph Wavelet Compressed Sensing with Scale-Aware Neural Recovery

Scientific machine learning methods such as neural operators and physics-informed neural networks have advanced engineering applications and inverse problems, but their training typically requires large volumes of simulated data. This makes data preparation and model training expensive. We propose Graph Wavelet Compressed Sensing (GWCS), a learning-based framework for offline compression of graph signals by representing them as sparse, interpretable wavelet-domain representations using the spectral graph wavelet transform. The framework combines a nonparametric multilevel importance sampler, which retains high-energy wavelet coefficients within each scale for a given compression ratio, with a scale-aware graph neural network that reconstructs the signal from the sparse coefficients. We evaluate the proposed framework on synthetic approximately band-limited graph signals over random graphs and four PDE simulation datasets over meshes, which include Turbulent Radiative Layer, Viscoelastic Instability, Kolmogorov Flow, and Dynamic Stall. We compare against graph signal sampling methods and graph autoencoder baselines. Results demonstrate that the framework achieves high reconstruction fidelity and substantial data compression compared to existing benchmarks.

cs.LG↗

arXiv2026

HypEHR: Hyperbolic Modeling of Electronic Health Records for Efficient Question Answering

Electronic health record (EHR) question answering is often handled by LLM-based pipelines that are costly to deploy and do not explicitly leverage the hierarchical structure of clinical data. Motivated by evidence that medical ontologies and patient trajectories exhibit hyperbolic geometry, we propose HypEHR, a compact Lorentzian model that embeds codes, visits, and questions in hyperbolic space and answers queries via geometry-consistent cross-attention with type-specific pointer heads. HypEHR is pretrained with next-visit diagnosis prediction and hierarchy-aware regularization to align representations with the ICD ontology. On two MIMIC-IV-based EHR-QA benchmarks, HypEHR approaches LLM-based methods while using far fewer parameters. Our code is publicly available at https://github.com/yuyuliu11037/HypEHR.

cs.AI↗

arXiv2026

HyperGuide: Hyperbolic Guidance for Efficient Multi-Step Reasoning in Large Language Models

Multi-step reasoning remains a central challenge for large language models: single-pass generation is efficient but lacks accuracy; tree-search methods explore multiple paths but are computation-heavy. We address this gap by distilling reasoning progress into a hyperbolic geometric signal that guides step-by-step generation. Our approach is motivated by a structural observation: in combinatorial reasoning trees, solution-bearing states are few while dead ends are exponentially numerous. The hyperbolic space matches this asymmetry, with compact volume near the origin and exponentially expanding capacity toward the boundary, so that distance-to-origin naturally encodes solution proximity while angular separation distinguishes branches requiring different next operations. We train a lightweight head to project LLM hidden states into this space, then fine-tune a low-rank adapter interactively on its own reasoning attempts to act on the injected signal. Across multiple benchmarks, the geometric signal yields consistent gains, with larger improvements on deeper reasoning chains. Our code is publicly available at https://github.com/yuyuliu11037/HyperGuide.

cs.AI↗

arXiv2026

Prediction of Magnetic Flux Evolution During Solar Active Region Emergence using Long Short-Term Memory Networks

Solar active regions (ARs) are the primary drivers of space weather events, making their early prediction crucial for operational forecasting systems. We develop machine learning models capable of predicting the evolution of magnetic flux during AR emergence using 1D time series of the continuum intensity and solar oscillation power maps for 53 active regions and their surrounding quiet-Sun areas. Each observable is sampled over a fixed 30.66°x30.66° field of view. These observations capture the temporal evolution of each active region and serve as inputs for training and validation of our MagFluxLSTM and MagFluxEnc-Dec models. The MagFluxLSTM architecture implements a single-stage standard Long-Short Term Memory (LSTM) network. MagFluxEnc-Dec represents an LSTM encoder-decoder with teacher forcing. To test and evaluate the models' performance, we use the continuum intensity and oscillation power maps (calculated for several frequency bands from Doppler velocity) as input to predict the magnetic flux. Among the top 100 hyperparameter configurations ranked by validation derivative RMSE, 98% correspond to MagFluxLSTM, compared to only 2% for MagFluxEnc-Dec. Thus, although the MagFluxEnc-Dec architecture has higher model complexity, it leads to poorer generalization to ARs outside the training set and less stable training than the simpler MagFluxLSTM, which can predict magnetic flux emergence 3-10 hours in advance within a 12-hour prediction window in both experimental and operational-type settings for the 5 testing active regions.

astro-ph.SR↗

arXiv2026

Implementation of a Near-Realtime Recording and Reporting System of Solar Radio Bursts

Strong solar activity is often accompanied by a variety of radio bursts. These bursts are valuable diagnostics of coronal and heliospheric processes and also have potential applications in space weather monitoring and forecasting. However, space weather applications require low-latency, high-sensitivity radio burst recording and reporting capabilities, which have remained limited. In this work, we present the development of a near-realtime radio burst recording and reporting system using the Owens Valley Radio Observatory Long Wavelength Array. The system directly clips data from a realtime buffer and streams them as a live radio dynamic spectrogram. These spectrograms are then processed by a deep-learning-based burst identification module for type III radio bursts. The identifier is based on a YOLO (You Only Look Once) architecture and is trained on synthetic type III radio bursts generated using a physics-based model to achieve accurate and robust detection. This system enables continuous realtime radio spectrum streaming and automatic reporting of type III radio bursts within approximately 10 seconds of their occurrence.

astro-ph.SR↗

arXiv2026

An AI-enabled tool for quantifying overlapping red blood cell sickling dynamics in microfluidic assays

Understanding sickle cell dynamics requires accurate identification of morphological transitions under diverse biophysical conditions, particularly in densely packed and overlapping cell populations. Here, we present an automated deep learning framework that integrates AI-assisted annotation, segmentation, classification, and instance counting to quantify red blood cell (RBC) populations across varying density regimes in time-lapse microscopy data. Experimental images were annotated using the Roboflow platform to generate labeled dataset for training an nnU-Net segmentation model. The trained network enables prediction of the temporal evolution of the sickle cell fraction, while a watershed algorithm resolves overlapping cells to enhance quantification accuracy. Despite requiring only a limited amount of labeled data for training, the framework achieves high segmentation performance, effectively addressing challenges associated with scarce manual annotations and cell overlap. By quantitatively tracking dynamic changes in RBC morphology, this approach can more than double the experimental throughput via densely packed cell suspensions, capture drug-dependent sickling behavior, and reveal distinct mechanobiological signatures of cellular morphological evolution. Overall, this AI-driven framework establishes a scalable and reproducible computational platform for investigating cellular biomechanics and assessing therapeutic efficacy in microphysiological systems.

cs.CV↗

arXiv2026

Forecasting Continuum Intensity for Solar Active Region Emergence Prediction using Transformers

Early and accurate prediction of solar active region (AR) emergence is crucial for space weather forecasting. Building on established Long Short-Term Memory (LSTM) based approaches for forecasting the continuum intensity decrease associated with AR emergence, this work expands the modeling with new architectures and targets. We investigate a sliding-window Transformer architecture to forecast continuum intensity evolution up to 12 hours ahead using data from 46 ARs observed by SDO/HMI. We conduct a systematic ablation study to evaluate two key components: (1) the inclusion of a temporal 1D convolutional (Conv1D) front-end and (2) a novel `Early Detection' architecture featuring attention biases and a timing-aware loss function. Our best-performing model, combining the Early Detection architecture without the Conv1D layer, achieved a Root Mean Square Error (RMSE) of 0.1189 (representing a 10.6% improvement over the LSTM baseline) and an average advance warning time of 4.73 hours (timing difference of -4.73h), even under a stricter emergence criterion than previous studies. While the Transformer demonstrates superior aggregate timing and accuracy, we note that this high-sensitivity detection comes with increased variance compared to smoother baseline models. However, this volatility is a necessary trade-off for operational warning systems: the model's ability to detect micro-changes in precursor signals enables significantly earlier detection, outweighing the cost of increased noise. Our results demonstrate that Transformer architectures modified with early detection biases, when used without temporal smoothing layers, provide a high-sensitivity alternative for forecasting AR emergence that prioritizes advance warning over statistical smoothness.

astro-ph.SR↗

arXiv2026

SolARED: Solar Active Region Emergence Dataset for Machine Learning Aided Predictions

The development of accurate forecasts of solar eruptive activity has become increasingly important for preventing potential impacts on space technologies and exploration. Therefore, it is crucial to detect Active Regions (ARs) before they start forming on the solar surface. This will enable the development of early-warning capabilities for upcoming space weather disturbances. For this reason, we prepared the Solar Active Region Emergence Dataset (SolARED). The dataset is derived from full-disk maps of the Doppler velocity, magnetic field, and continuum intensity, obtained by the Helioseismic and Magnetic Imager (HMI) onboard the Solar Dynamics Observatory (SDO). SolARED includes time series of remapped, tracked, and binned data that characterize the evolution of acoustic power of solar oscillations, unsigned magnetic flux, and continuum intensity for 50 large ARs before, during, and after their emergence on the solar surface, as well as surrounding areas observed on the solar disc between 2010 and 2023. The resulting ML-ready SolARED dataset is designed to support enhancements of predictive capabilities, enabling the development of operational forecasts for the emergence of active regions. The SolARED dataset is available at https://sun.njit.edu/sarportal/, through an interactive visualization web application.

astro-ph.SR↗

arXiv2025

Hyperbolic Large Language Models

Large language models (LLMs) have achieved remarkable success and demonstrated superior performance across various tasks, including natural language processing (NLP), weather forecasting, biological protein folding, text generation, and solving mathematical problems. However, many real-world data exhibit highly non-Euclidean latent hierarchical anatomy, such as protein networks, transportation networks, financial networks, brain networks, and linguistic structures or syntactic trees in natural languages. Effectively learning intrinsic semantic entailment and hierarchical relationships from these raw, unstructured input data using LLMs remains an underexplored area. Due to its effectiveness in modeling tree-like hierarchical structures, hyperbolic geometry -- a non-Euclidean space -- has rapidly gained popularity as an expressive latent representation space for complex data modeling across domains such as graphs, images, languages, and multi-modal data. Here, we provide a comprehensive and contextual exposition of recent advancements in LLMs that leverage hyperbolic geometry as a representation space to enhance semantic representation learning and multi-scale reasoning. Specifically, the paper presents a taxonomy of the principal techniques of Hyperbolic LLMs (HypLLMs) in terms of four main categories: (1) hyperbolic LLMs through exp/log maps; (2) hyperbolic fine-tuned models; (3) fully hyperbolic LLMs, and (4) hyperbolic state-space models. We also explore crucial potential applications and outline future research directions. A repository of key papers, models, datasets, and code implementations is available at https://github.com/sarangp2402/Hyperbolic-LLM-Models.

cs.AI↗

arXiv2025

RGE-GCN: Recursive Gene Elimination with Graph Convolutional Networks for RNA-seq based Early Cancer Detection

Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to capture the complex relationships between genes. In this study, we introduce RGE-GCN (Recursive Gene Elimination with Graph Convolutional Networks), a framework that combines feature selection and classification in a single pipeline. Our approach builds a graph from gene expression profiles, uses a Graph Convolutional Network to classify cancer versus normal samples, and applies Integrated Gradients to highlight the most informative genes. By recursively removing less relevant genes, the model converges to a compact set of biomarkers that are both interpretable and predictive. We evaluated RGE-GCN on synthetic data as well as real-world RNA-seq cohorts of lung, kidney, and cervical cancers. Across all datasets, the method consistently achieved higher accuracy and F1-scores than standard tools such as DESeq2, edgeR, and limma-voom. Importantly, the selected genes aligned with well-known cancer pathways including PI3K-AKT, MAPK, SUMOylation, and immune regulation. These results suggest that RGE-GCN shows promise as a generalizable approach for RNA-seq based early cancer detection and biomarker discovery (https://rce-gcn.streamlit.app/ ).

cs.LG↗

arXiv2025

Hierarchical Mamba Meets Hyperbolic Geometry: A New Paradigm for Structured Language Embeddings

Selective state-space models excel at long-sequence modeling, but their capacity for language representation -- in complex hierarchical reasoning -- remains underexplored. Most large language models rely on \textit{flat} Euclidean embeddings, limiting their ability to capture latent hierarchies. To address this, we propose {\it Hierarchical Mamba (HiM)}, integrating efficient Mamba2 with hyperbolic geometry to learn hierarchy-aware language embeddings for deeper linguistic understanding. Mamba2-processed sequences are projected to the Poincaré ball or Lorentzian manifold with ``learnable'' curvature, optimized with a hyperbolic loss. Our HiM model facilitates the capture of relational distances across varying hierarchical levels, enabling effective long-range reasoning for tasks like mixed-hop prediction and multi-hop inference in hierarchical classification. Experimental results show both HiM variants effectively capture hierarchical relationships across four linguistic and medical datasets, surpassing Euclidean baselines, with HiM-Poincaré providing fine-grained distinctions with higher h-norms, while HiM-Lorentz offers more stable, compact, and hierarchy-preserving embeddings-favoring robustness. The source code is publicly available at https://github.com/BerryByte/HiM.

cs.CL↗

arXiv2025

Arcee: Differentiable Recurrent State Chain for Generative Vision Modeling with Mamba SSMs

State-space models (SSMs), Mamba in particular, are increasingly adopted for long-context sequence modeling, providing linear-time aggregation via an input-dependent, causal selective-scan operation. Along this line, recent "Mamba-for-vision" variants largely explore multiple scan orders to relax strict causality for non-sequential signals (e.g., images). Rather than preserving cross-block memory, the conventional formulation of the selective-scan operation in Mamba reinitializes each block's state-space dynamics from zero, discarding the terminal state-space representation (SSR) from the previous block. Arcee, a cross-block recurrent state chain, reuses each block's terminal state-space representation as the initial condition for the next block. Handoff across blocks is constructed as a differentiable boundary map whose Jacobian enables end-to-end gradient flow across terminal boundaries. Key to practicality, Arcee is compatible with all prior "vision-mamba" variants, parameter-free, and incurs constant, negligible cost. As a modeling perspective, we view terminal SSR as a mild directional prior induced by a causal pass over the input, rather than an estimator of the non-sequential signal itself. To quantify the impact, for unconditional generation on CelebA-HQ (256$\times$256) with Flow Matching, Arcee reduces FID$\downarrow$ from $82.81$ to $15.33$ ($5.4\times$ lower) on a single scan-order Zigzag Mamba baseline. Efficient CUDA kernels and training code will be released to support rigorous and reproducible research.

cs.CV↗

arXiv2025

Automatic Classification of Circulating Blood Cell Clusters based on Multi-channel Flow Cytometry Imaging

Circulating blood cell clusters (CCCs) containing red blood cells (RBCs), white blood cells(WBCs), and platelets are significant biomarkers linked to conditions like thrombosis, infection, and inflammation. Flow cytometry, paired with fluorescence staining, is commonly used to analyze these cell clusters, revealing cell morphology and protein profiles. While computational approaches based on machine learning have advanced the automatic analysis of single-cell flow cytometry images, there is a lack of effort to build tools to automatically analyze images containing CCCs. Unlike single cells, cell clusters often exhibit irregular shapes and sizes. In addition, these cell clusters often consist of heterogeneous cell types, which require multi-channel staining to identify the specific cell types within the clusters. This study introduces a new computational framework for analyzing CCC images and identifying cell types within clusters. Our framework uses a two-step analysis strategy. First, it categorizes images into cell cluster and non-cluster groups by fine-tuning the You Only Look Once(YOLOv11) model, which outperforms traditional convolutional neural networks (CNNs), Vision Transformers (ViT). Then, it identifies cell types by overlaying cluster contours with regions from multi-channel fluorescence stains, enhancing accuracy despite cell debris and staining artifacts. This approach achieved over 95% accuracy in both cluster classification and phenotype identification. In summary, our automated framework effectively analyzes CCC images from flow cytometry, leveraging both bright-field and fluorescence data. Initially tested on blood cells, it holds potential for broader applications, such as analyzing immune and tumor cell clusters, supporting cellular research across various diseases.

cs.CV↗

arXiv2025

BrainATCL: Adaptive Temporal Brain Connectivity Learning for Functional Link Prediction and Age Estimation

Functional Magnetic Resonance Imaging (fMRI) is an imaging technique widely used to study human brain activity. fMRI signals in areas across the brain transiently synchronise and desynchronise their activity in a highly structured manner, even when an individual is at rest. These functional connectivity dynamics may be related to behaviour and neuropsychiatric disease. To model these dynamics, temporal brain connectivity representations are essential, as they reflect evolving interactions between brain regions and provide insight into transient neural states and network reconfigurations. However, conventional graph neural networks (GNNs) often struggle to capture long-range temporal dependencies in dynamic fMRI data. To address this challenge, we propose BrainATCL, an unsupervised, nonparametric framework for adaptive temporal brain connectivity learning, enabling functional link prediction and age estimation. Our method dynamically adjusts the lookback window for each snapshot based on the rate of newly added edges. Graph sequences are subsequently encoded using a GINE-Mamba2 backbone to learn spatial-temporal representations of dynamic functional connectivity in resting-state fMRI data of 1,000 participants from the Human Connectome Project. To further improve spatial modeling, we incorporate brain structure and function-informed edge attributes, i.e., the left/right hemispheric identity and subnetwork membership of brain regions, enabling the model to capture biologically meaningful topological patterns. We evaluate our BrainATCL on two tasks: functional link prediction and age estimation. The experimental results demonstrate superior performance and strong generalization, including in cross-session prediction scenarios.

cs.LG↗

arXiv2025

Quantum Cognition Machine Learning for Forecasting Chromosomal Instability

The accurate prediction of chromosomal instability from the morphology of circulating tumor cells (CTCs) enables real-time detection of CTCs with high metastatic potential in the context of liquid biopsy diagnostics. However, it presents a significant challenge due to the high dimensionality and complexity of single-cell digital pathology data. Here, we introduce the application of Quantum Cognition Machine Learning (QCML), a quantum-inspired computational framework, to estimate morphology-predicted chromosomal instability in CTCs from patients with metastatic breast cancer. QCML leverages quantum mechanical principles to represent data as state vectors in a Hilbert space, enabling context-aware feature modeling, dimensionality reduction, and enhanced generalization without requiring curated feature selection. QCML outperforms conventional machine learning methods when tested on out of sample verification CTCs, achieving higher accuracy in identifying predicted large-scale state transitions (pLST) status from CTC-derived morphology features. These preliminary findings support the application of QCML as a novel machine learning tool with superior performance in high-dimensional, low-sample-size biomedical contexts. QCML enables the simulation of cognition-like learning for the identification of biologically meaningful prediction of chromosomal instability from CTC morphology, offering a novel tool for CTC classification in liquid biopsy.

q-bio.QM↗

arXiv2025

Quantum Geometry of Data

We demonstrate how Quantum Cognition Machine Learning (QCML) encodes data as quantum geometry. In QCML, features of the data are represented by learned Hermitian matrices, and data points are mapped to states in Hilbert space. The quantum geometry description endows the dataset with rich geometric and topological structure - including intrinsic dimension, quantum metric, and Berry curvature - derived directly from the data. QCML captures global properties of data, while avoiding the curse of dimensionality inherent in local methods. We illustrate this on a number of synthetic and real-world examples. Quantum geometric representation of QCML could advance our understanding of cognitive phenomena within the framework of quantum cognition.

cs.LG↗

arXiv2025

A Comparative Study on Dynamic Graph Embedding based on Mamba and Transformers

Dynamic graph embedding has emerged as an important technique for modeling complex time-evolving networks across diverse domains. While transformer-based models have shown promise in capturing long-range dependencies in temporal graph data, they face scalability challenges due to quadratic computational complexity. This study presents a comparative analysis of dynamic graph embedding approaches using transformers and the recently proposed Mamba architecture, a state-space model with linear complexity. We introduce three novel models: TransformerG2G augment with graph convolutional networks, \mathcal{DG}-Mamba, and \mathcal{GDG}-Mamba with graph isomorphism network edge convolutions. Our experiments on multiple benchmark datasets demonstrate that Mamba-based models achieve comparable or superior performance to transformer-based approaches in link prediction tasks while offering significant computational efficiency gains on longer sequences. Notably, \mathcal{DG}-Mamba variants consistently outperform transformer-based models on datasets with high temporal variability, such as UCI, Bitcoin, and Reality Mining, while maintaining competitive performance on more stable graphs like SBM. We provide insights into the learned temporal dependencies through analysis of attention weights and state matrices, revealing the models' ability to capture complex temporal patterns. By effectively combining state-space models with graph neural networks, our work addresses key limitations of previous approaches and contributes to the growing body of research on efficient temporal graph representation learning. These findings offer promising directions for scaling dynamic graph embedding to larger, more complex real-world networks, potentially enabling new applications in areas such as social network analysis, financial modeling, and biological system dynamics.

cs.LG↗

arXiv2024

Robust estimation of the intrinsic dimension of data sets with quantum cognition machine learning

We propose a new data representation method based on Quantum Cognition Machine Learning and apply it to manifold learning, specifically to the estimation of intrinsic dimension of data sets. The idea is to learn a representation of each data point as a quantum state, encoding both local properties of the point as well as its relation with the entire data. Inspired by ideas from quantum geometry, we then construct from the quantum states a point cloud equipped with a quantum metric. The metric exhibits a spectral gap whose location corresponds to the intrinsic dimension of the data. The proposed estimator is based on the detection of this spectral gap. When tested on synthetic manifold benchmarks, our estimates are shown to be robust with respect to the introduction of point-wise Gaussian noise. This is in contrast to current state-of-the-art estimators, which tend to attribute artificial ``shadow dimensions'' to noise artifacts, leading to overestimates. This is a significant advantage when dealing with real data sets, which are inevitably affected by unknown levels of noise. We show the applicability and robustness of our method on real data, by testing it on the ISOMAP face database, MNIST, and the Wisconsin Breast Cancer Dataset.

stat.ML↗