arXiv subjects

Lei Xing

Publications and source records attributed to Lei Xing.

At least 19 recordsLinked to original sources

arXiv2026

State-Space Model-Enabled Reinforcement Learning for Magnetic Configuration Controlon EXL-50U

Accurate feedback control of the plasma current ($I_p$) and centroid position $(R_c,Z_c)$ is essential for the stable operation of spherical torus (ST) plasmas. Conventional proportional-integral-derivative (PID) controllers require extensive manual tuning and struggle with the fast, strongly coupled dynamics that arise as plasma performance improves. Reinforcement learning (RL) has recently emerged as a promising alternative to such complex magnetic control problems, yet its practical deployment on ST devices remains challenging. This paper presents a practical RL controller for the EXL-50U ST, trained within a rigid RZIP state-space model (SSM) that enables efficient offline policy learning. A lightweight plasma position reconstructor is developed to estimate $(R_c,Z_c)$ from magnetic probe signals within the real-time control cycle. The trained policy is seamlessly deployed on the EXL-50U plasma control system, achieving stable regulation of $I_p$ and $(R_c,Z_c)$ and sustaining discharges up to 650 ms under RL control. These results demonstrate the feasibility and practical potential of model-informed RL for magnetic configuration control in ST devices, offering a promising direction beyond conventional PID-based schemes.

physics.plasm-ph↗

arXiv2026

Advantage-level Aggregation Reinforcement Learning for X-point Target Magnetic Configuration Control in an EXL-50U Experiment-Calibrated Simulation Environment

Managing divertor heat loads is a central challenge for compact, high-power tokamaks. To increase local flux expansion and decouple the dissipation volume from the core, EHL-2 adopts the X-point target (XPT) divertor. This requires the secondary X-point to remain on the divertor leg; displacement degrades the topology and exhaust geometry. Current experiments, including EXL-50U discharges, rely on precomputed feedforward waveforms with PID loops on global quantities. Lacking dedicated closed-loop feedback for the secondary null, XPT operation is repeatable but not routine. We formulate XPT feedback as a multi-objective reinforcement learning (RL) control problem in a free-boundary environment calibrated to EXL-50U discharge #13906. To address strong coupling among plasma current, shape, and null constraints - where reward scalarisation collapses objective-specific temporal credit - we develop Advantage Aggregation (AdvA). AdvA preserves objective-wise temporal credit before worst-objective-aware nonlinear scalarisation and introduces a residual correction to policy updates. AdvA-PPO is evaluated against Reward-PPO and a feedforward-plus-PID baseline under nominal operation, measurement uncertainties, and unseen initial equilibria. On a 500 ms rollout, AdvA-PPO raises the mean worst-channel score from 0.23 to 0.81 over Reward-PPO, reducing X-point flux RMSE by ~20x. Under combined measurement uncertainties, it is the only learned controller completing the horizon while retaining a usable XPT shape. Multi-initialization fine-tuning enables a single AdvA-PPO policy to complete full-horizon operation across divertor and limiter initial equilibria. These results provide a simulation-based foundation for future real-time XPT validation on EXL-50U.

physics.plasm-ph↗

arXiv2026

Reinforcement learning for vertical position control on the EXL-50U spherical tokamak

Vertical position control is essential for sustaining high-performance operation in spherical tokamaks, where increased plasma elongation introduces stringent requirements on fast and robust stabilization. This work presents an experimentally validated reinforcement-learning(RL)-based vertical position control framework for the EXL-50U spherical tokamak. A high-fidelity discharge-reconstructed simulation environment is developed by integrating physics-based plasma-circuit models with experimental equilibrium information, enabling systematic controller synthesis and sim-to-real evaluation. Within this framework, RL is benchmarked in simulation against operational proportional--integral--derivative (PID) and model-based linear quadratic regulator (LQR) controllers under identical plant dynamics, actuator constraints, and measurement imperfections.Simulation results show that RL achieves tracking accuracy comparable to PID with consistently lower vertical-stabilization coil effort, while lightweight integral compensation improves robustness against residual model--plant mismatch. The RL controller is subsequently deployed on EXL-50U for closed-loop experiments. Across more than ten discharges with RL takeover, stable vertical regulation is achieved within the controlled windows. For seven representative discharges, RL maintains millimetre-scale tracking accuracy comparable to the operational PID controller (MAE typically ~ 1-5 mm) while consistently reducing actuator effort. These results demonstrate the feasibility of learning-based plasma control on a real spherical tokamak and establish a practical pathway toward future fusion control systems.

physics.plasm-ph↗

arXiv2026

A vision foundation model for single-cell biology via spatial gene cartography

Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens. This discards the relationships among genes and often the magnitude of their expression. We present scVision, a vision foundation model that instead renders each cell as a continuous image. Using optimal transport, it places genes at fixed positions on a single shared, pan-tissue layout so that co-expressed genes become spatial neighbours, turning a transcriptome into an image in which gene programs appear as local texture. We pretrain a vision transformer by masked image modelling on 72 million human cells and use the frozen encoder with no fine-tuning. In zero-shot evaluations on six independent, held-out studies, scVision is the most accurate cell-type annotator and recovers gene programs without supervision, ahead of existing foundation models and classical baselines; on multi-study integration it matches the strongest token-based model while conserving the most biological structure, without ever seeing a batch label. Permuting the gene layout with the network fixed sharply lowers accuracy, more than removing the vision transformer itself, showing that biologically meaningful position, not the network, carries the signal. By preserving expression magnitude and gene relationships, scVision reframes single-cell representation learning as a vision problem, connecting it to the mature methods of computer vision.

q-bio.QM↗

arXiv2026

Dosimetric characterization of a nanophotonic scintillator and applications to real-time in-vivo total body irradiation dosimetry

Purpose: Recent advances in metasurface photonics and manufacturing have enabled a nanophotonic surface coating to be applied to conventional scintillators, which has been shown to significantly improve light yield. However, the dosimetric properties of such coatings has not been established. We performed the first dosimetric characterization of a nanophotonic scintillator and explored clinical application to real-time in-vivo total body irradiation (TBI) dosimetry. Methods: A 4.5x1.5 cm cerium-doped yttrium aluminum garnet (YAG:Ce) scintillator, half patterned with the nanophotonic structure, half left unpatterned, enabled direct comparison between conventional and nanophotonic surfaces. The scintillator was placed in a 3D-printed light-tight box with an off-axis CMOS camera and irradiated with a clinical linear accelerator. Absolute dosimetry was done with dose-calibrated radiochromic film. For TBI, the scintillator was positioned on an anthropomorphic phantom in a TBI booth, with signal measured by both CMOS and consumer-grade phone cameras under different room lighting conditions. Results: The nanophotonic scintillator showed a 4.1x increase in signal and a 3.7x increase in contrast-to-noise ratio versus the conventional scintillator. Both scintillators exhibited dose-rate independence and linear dose response, with modest energy dependence. For TBI, the nanophotonic scintillator produced a clearly detectable signal with both CMOS and phone cameras, whereas the conventional scintillator signal was undetectable. Conclusions: Nanophotonic structures significantly enhance light output of conventional scintillators without impacting their dosimetric properties. Nanophotonic scintillators may enable real-time in-vivo TBI dosimetry. Future work should investigate this technology for improved dosimetry equipment and X-ray imaging detectors.

physics.med-ph↗

arXiv2026

AutoResearch AI: Towards AI-Powered Research Automation for Scientific Discovery

Scientific research is being reshaped by AI systems that move beyond isolated assistance toward longer-horizon workflows spanning literature grounding, hypothesis generation, experimentation, validation, reporting, and revision. This shift marks a transition from task-level AI for science to workflow-level research automation. Yet current systems remain fragmented, differing in autonomy, domain scope, execution environment, validation mechanism, and human oversight, while still struggling with evidence preservation, reproducibility, weak-direction rejection, provenance tracking, cross-domain robustness, and accountable scientific closure. This survey examines these developments through AutoResearch, defined as the developmental spectrum of AI-powered scientific workflow automation. Within it, Vibe Research denotes the human-steered region of prompt-based assistance and human-verified execution, whereas emerging AI-led systems coordinate larger portions of the discovery loop without achieving robust autonomy. We analyze how research systems redistribute control, evidence, execution, validation, and accountability across workflows and organize the field around five workflow conditions: literature and research grounding; hypothesis formation and planning; experimentation and tool use; feedback, validation, and review; and reporting and knowledge communication. We further synthesize AI scientist systems, mixed-initiative co-research frameworks, benchmarks, domain deployments, and open-source infrastructures. Finally, we propose five evaluation dimensions--novelty, validity, impact, reliability, and provenance--and show that AutoResearch autonomy is domain-conditioned, being more credible in structured, executable, and rapidly verifiable settings but limited in embodied, delayed, heterogeneous, ethical, or institutionally accountable contexts.

cs.AI↗

arXiv2026

Knowledge Graph Modulated Deep Learning for Limited-Sample Clinical Data Analysis

Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease progression. Much of this knowledge is naturally represented as graphs. However, most biomedical AI models cannot directly use graph-encoded biological knowledge and instead require compressed low-dimensional representations, which can lose important structure and reduce performance, especially in limited-sample clinical studies. Here, we introduce Graph-in-Graph (GiG), a knowledge graph-modulated deep learning framework for data-efficient clinical prediction. GiG represents each patient as a standalone modular graph, in which curated biological knowledge graphs define edges and patient-specific measurements, such as gene expression, define node features. This design allows multiple biological knowledge graphs to be integrated while preserving gene-gene interactions and pathway topology during patient-level representation learning. Across cohorts comprising nearly 9,700 patients and five clinical tasks, including liquid biopsy cancer detection, prostate cancer diagnosis, and 32-class pan-cancer classification, GiG consistently outperforms traditional and state-of-the-art methods, with the largest gains in limited-sample settings. On the challenging prostate cancer diagnosis task, GiG improves macro-F1 by up to 49 percentage points relative to competing methods. Control experiments replacing real pathway graphs with random topologies confirm that these gains arise from biologically grounded knowledge graph structure rather than graph modeling alone. These findings show that knowledge graph-modulated deep learning can improve robustness, interpretability, and sample efficiency in clinical data analysis, and provide a principled framework for integrating biological knowledge graphs into predictive modeling.

cs.LG↗

arXiv2026

Training-Time Optical Priors for Wireless Capsule Endoscopy Classification: Hemoglobin-Aware Input Fusion with Cross-Vendor Evaluation

Gastrointestinal cancers cause approximately 3.4 million deaths annually, and early small-bowel lesions are easily missed at wireless capsule endoscopy (WCE). RGB-trained WCE classifiers conflate hemoglobin contrast with bile staining and illumination falloff, limiting sensitivity to small-vessel vascular findings such as Lymphangiectasia. We introduce a physics-informed framework that injects an analytic, Monte-Carlo-inspired hemoglobin prior into a standard classifier purely at training time -- to our knowledge the first use of an explicit optical light-transport prior in WCE classification. On Kvasir-Capsule (47,238 frames, 43 patients, 11 evaluable classes; patient-disjoint split) we evaluate, across six seeds against an RGB-only EfficientNet-B0 baseline, a five-channel input-fusion variant feeding the prior alongside RGB, a distillation variant that runs on plain three-channel RGB at inference, and a three-stream extension adding a temporal Transformer and an autoencoder-residual stream; we replicate across ResNet-18 and ConvNeXt-Tiny and assess cross-vendor zero-shot transfer on the public Galar cohort. Input fusion lifts cross-seed macro-AUC from 0.760 to 0.783 (5/6 seeds positive); distillation reaches 0.773; the three-stream model reaches 0.804 (+0.044 over baseline, paired DeLong p < 0.0001). Lymphangiectasia AUC rises from 0.238 to 0.337, sign-consistent across all six seeds. A four-variant ablation reveals a parameterization-mechanism boundary: only the spatial-channel form lifts. Cross-vendor zero-shot on Galar retains about 60% of the lift. The distillation variant deploys on plain RGB with a free interpretability heatmap, and we release GalKva-2026, a paired cross-vendor benchmark.

cs.CV↗

arXiv2026

Toward a universal foundation model for graph-structured data

Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs. Despite their importance, currently there is not a broadly reusable foundation model available for graph analysis comparable to those that have transformed language and vision. Existing graph neural networks are typically trained on a single dataset and learn representations specific only to that graph's node features, topology, and label space, limiting their ability to transfer across domains. This lack of generalization is particularly problematic in biology and medicine, where networks vary substantially across cohorts, assays, and institutions. Here we introduce a graph foundation model designed to learn transferable structural representations that are not specific to specific node identities or feature schemes. Our approach leverages feature-agnostic graph properties, including degree statistics, centrality measures, community structure indicators, and diffusion-based signatures, and encodes them as structural prompts. These prompts are integrated with a message-passing backbone to embed diverse graphs into a shared representation space. The model is pretrained once on heterogeneous graphs and subsequently reused on unseen datasets with minimal adaptation. Across multiple benchmarks, our pretrained model matches or exceeds strong supervised baselines while demonstrating superior zero-shot and few-shot generalization on held-out graphs. On the SagePPI benchmark, supervised fine-tuning of the pretrained backbone achieves a mean ROC-AUC of 95.5%, a gain of 21.8% over the best supervised message-passing baseline. The proposed technique thus provides a unique approach toward reusable, foundation-scale models for graph-structured data in biomedical and network science applications.

cs.LG↗

arXiv2026

Towards a Medical AI Scientist

Autonomous systems that generate scientific hypotheses, conduct experiments, and draft manuscripts have recently emerged as a promising paradigm for accelerating discovery. However, existing AI Scientists remain largely domain-agnostic, limiting their applicability to clinical medicine, where research is required to be grounded in medical evidence with specialized data modalities. In this work, we introduce Medical AI Scientist, the first autonomous research framework tailored to clinical autonomous research. It enables clinically grounded ideation by transforming extensively surveyed literature into actionable evidence through clinician-engineer co-reasoning mechanism, which improves the traceability of generated research ideas. It further facilitates evidence-grounded manuscript drafting guided by structured medical compositional conventions and ethical policies. The framework operates under 3 research modes, namely paper-based reproduction, literature-inspired innovation, and task-driven exploration, each corresponding to a distinct level of automated scientific inquiry with progressively increasing autonomy. Comprehensive evaluations by both large language models and human experts demonstrate that the ideas generated by the Medical AI Scientist are of substantially higher quality than those produced by commercial LLMs across 171 cases, 19 clinical tasks, and 6 data modalities. Meanwhile, our system achieves strong alignment between the proposed method and its implementation, while also demonstrating significantly higher success rates in executable experiments. Double-blind evaluations by human experts and the Stanford Agentic Reviewer suggest that the generated manuscripts approach MICCAI-level quality, while consistently surpassing those from ISBI and BIBM. The proposed Medical AI Scientist highlights the potential of leveraging AI for autonomous scientific discovery in healthcare.

cs.AI↗

arXiv2026

Vision-based Deep Learning Analysis of Unordered Biomedical Tabular Datasets via Optimal Spatial Cartography

Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or sequences, however, tabular datasets lack intrinsic spatial organization: features are treated as unordered dimensions, and their relationships must be inferred implicitly by the model. This limits the ability of vision architectures to exploit local structure and higher-order feature interactions in non-spatial biomedical data. Here we introduce Dynamic Feature Mapping (Dynomap), an end-to-end deep learning framework that learns a task-optimized spatial topology of features directly from data. Dynomap jointly optimizes feature placement and prediction through a fully differentiable rendering mechanism, without relying on heuristics, predefined groupings, or external priors. By transforming high-dimensional tabular vectors into learned feature maps, Dynomap enables vision-based models to operate effectively on unordered biomedical inputs. Across multiple clinical and biological datasets, Dynomap consistently outperformed classical machine learning, modern deep tabular models, and existing vector-to-image approaches. In liquid biopsy data, Dynomap organized clinically relevant gene signatures into coherent spatial patterns and improved multiclass cancer subtype prediction accuracy by up to 18%. In a Parkinson disease voice dataset, it clustered disease-associated acoustic descriptors and improved accuracy by up to 8%. Similar gains and interpretable feature organization were observed in additional biomedical datasets. These results establish Dynomap as a general strategy for bridging tabular and vision-based deep learning and for uncovering structured, clinically relevant patterns in high-dimensional biomedical data.

cs.LG↗

arXiv2026

Cerebra: A Multidisciplinary AI Board for Multimodal Dementia Characterization and Risk Assessment

Modern clinical practice increasingly depends on reasoning over heterogeneous, evolving, and incomplete patient data. Although recent advances in multimodal foundation models have improved performance on various clinical tasks, most existing models remain static, opaque, and poorly aligned with real-world clinical workflows. We present Cerebra, an interactive multi-agent AI team that coordinates specialized agents for EHR, clinical notes, and medical imaging analysis. These outputs are synthesized into a clinician-facing dashboard that combines visual analytics with a conversational interface, enabling clinicians to interrogate predictions and contextualize risk at the point of care. Cerebra supports privacy-preserving deployment by operating on structured representations and remains robust when modalities are incomplete. We evaluated Cerebra using a massive multi-institutional dataset spanning 3 million patients from four independent healthcare systems. Cerebra consistently outperformed both state-of-the-art single-modality models and large multimodal language model baselines. In dementia risk prediction, it achieved AUROCs up to 0.80, compared with 0.74 for the strongest single-modality model and 0.68 for language model baselines. For dementia diagnosis, it achieved an AUROC of 0.86, and for survival prediction, a C-index of 0.81. In a reader study with experienced physicians, Cerebra significantly improved expert performance, increasing accuracy by 17.5 percentage points in prospective dementia risk estimation. These results demonstrate Cerebra's potential for interpretable, robust decision support in clinical care.

cs.AI↗

arXiv2026

Suppressing Prior-Comparison Hallucinations in Radiology Report Generation via Semantically Decoupled Latent Steering

Automated radiology report generation using vision-language models (VLMs) is limited by the risk of prior-comparison hallucination, where the model generates historical findings unsupported by the current study. We address this challenge with a training-free, inference-time control framework termed Semantically Decoupled Latent Steering (SDLS). Unlike generic activation steering, which often suffers from semantic entanglement, our approach constructs a semantic-free intervention vector via large language model (LLM)-driven semantic decomposition followed by $QR$-based orthogonalization. This orthogonalization step is critical. It leverages geometric constraints to filter out the clinical semantics often entangled in standard principal component analysis (PCA) directions, ensuring that the steering vector targets only the ``historical comparison" axis. We validate our method on the BiomedGPT foundation model, demonstrating that it overcomes the trade-off between hallucination suppression and clinical accuracy. Extensive experiments on MIMIC-CXR, and zero-shot transfer evaluation on CheXpert Plus and IU-Xray, demonstrate the robustness of our approach. Quantitative evaluations on MIMIC-CXR show that our approach significantly reduces the probability of historical hallucinations (FilBERT score decreases from 0.2373 to 0.1889) and improves clinical label fidelity (CheXpert macro-F1 increases from 0.2242 to 0.3208). Supplementary evaluations confirm that the structural integrity of the clinical narrative is maintained.

cs.CV↗

arXiv2026

Redefining the Down-Sampling Scheme of U-Net for Precision Biomedical Image Segmentation

U-Net architectures have been instrumental in advancing biomedical image segmentation (BIS) but often struggle with capturing long-range information. One reason is the conventional down-sampling techniques that prioritize computational efficiency at the expense of information retention. This paper introduces a simple but effective strategy, we call it Stair Pooling, which moderates the pace of down-sampling and reduces information loss by leveraging a sequence of concatenated small and narrow pooling operations in varied orientations. Specifically, our method modifies the reduction in dimensionality within each 2D pooling step from $\frac{1}{4}$ to $\frac{1}{2}$. This approach can also be adapted for 3D pooling to preserve even more information. Such preservation aids the U-Net in more effectively reconstructing spatial details during the up-sampling phase, thereby enhancing its ability to capture long-range information and improving segmentation accuracy. Extensive experiments on three BIS benchmarks demonstrate that the proposed Stair Pooling can increase both 2D and 3D U-Net performance by an average of 3.8\% in Dice scores. Moreover, we leverage the transfer entropy to select the optimal down-sampling paths and quantitatively show how the proposed Stair Pooling reduces the information loss.

cs.CV↗

arXiv2026

Uncovering spatial tissue domains and cell types in spatial omics through cross-scale profiling of cellular and genomic interactions

Cellular identity and function are linked to both their intrinsic genomic makeup and extrinsic spatial context within the tissue microenvironment. Spatial transcriptomics (ST) offers an unprecedented opportunity to study this, providing in situ gene expression profiles at single-cell resolution and illuminating the spatial and functional organization of cells within tissues. However, a significant hurdle remains: ST data is inherently noisy, large, and structurally complex. This complexity makes it intractable for existing computational methods to effectively capture the interplay between spatial interactions and intrinsic genomic relationships, thus limiting our ability to discern critical biological patterns. Here, we present CellScape, a deep learning framework designed to overcome these limitations for high-performance ST data analysis and pattern discovery. CellScape jointly models cellular interactions in tissue space and genomic relationships among cells, producing comprehensive representations that seamlessly integrate spatial signals with underlying gene regulatory mechanisms. This technique uncovers biologically informative patterns that improve spatial domain segmentation and supports comprehensive spatial cellular analyses across diverse transcriptomics datasets, offering an accurate and versatile framework for deep analysis and interpretation of ST data.w

cs.LG↗

arXiv2026

Reshaping Action Error Distributions for Reliable Vision-Language-Action Models

In robotic manipulation, vision-language-action (VLA) models have emerged as a promising paradigm for learning generalizable and scalable robot policies. Most existing VLA frameworks rely on standard supervised objectives, typically cross-entropy for discrete actions and mean squared error (MSE) for continuous action regression, which impose strong pointwise constraints on individual predictions. In this work, we focus on continuous-action VLA models and move beyond conventional MSE-based regression by reshaping action error distributions during training. Drawing on information-theoretic principles, we introduce Minimum Error Entropy (MEE) into modern VLA architectures and propose a trajectory-level MEE objective, together with two weighted variants, combined with MSE for continuous-action VLA training. We evaluate our approaches across standard, few-shot, and noisy settings on multiple representative VLA architectures, using simulation benchmarks such as LIBERO and SimplerEnv as well as real-world robotic manipulation tasks. Experimental results demonstrate consistent improvements in success rates and robustness across these settings. Under imbalanced data regimes, the gains persist within a well-characterized operating range, while incurring negligible additional training cost and no impact on inference efficiency. We further provide theoretical analyses that explain why MEE-based supervision is effective and characterize its practical range. Project Page: https://cognition2actionlab.github.io/VLA-TMEE.github.io/

cs.RO↗

arXiv2026

Latent Reasoning VLA: Latent Thinking and Prediction for Vision-Language-Action Models

Vision-Language-Action (VLA) models benefit from chain-of-thought (CoT) reasoning, but existing approaches incur high inference overhead and rely on discrete reasoning representations that mismatch continuous perception and control. We propose Latent Reasoning VLA (LaRA-VLA), a unified VLA framework that internalizes multi-modal CoT reasoning into continuous latent representations for embodied action. LaRA-VLA performs unified reasoning and prediction in latent space, eliminating explicit CoT generation at inference time and enabling efficient, action-oriented control. To realize latent embodied reasoning, we introduce a curriculum-based training paradigm that progressively transitions from explicit textual and visual CoT supervision to latent reasoning, and finally adapts latent reasoning dynamics to condition action generation. We construct two structured CoT datasets and evaluate LaRA-VLA on both simulation benchmarks and long-horizon real-robot manipulation tasks. Experimental results show that LaRA-VLA consistently outperforms state-of-the-art VLA methods while reducing inference latency by up to 90\% compared to explicit CoT-based approaches, demonstrating latent reasoning as an effective and efficient paradigm for real-time embodied control. Project Page: https://loveju1y.github.io/Latent-Reasoning-VLA/

cs.RO↗

arXiv2025

Transformation of Biological Networks into Images via Semantic Cartography for Visual Interpretation and Scalable Deep Analysis

Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for understanding health and disease, yet their scale and complexity represent a daunting challenge for current computational methods. Traditional biological network analysis methods, including deep learning approaches, while powerful, face inherent challenges such as limited scalability, oversmoothing long-range dependencies, difficulty in multimodal integration, expressivity bounds, and poor interpretability. We present Graph2Image, a framework that transforms large biological networks into sets of two-dimensional images by spatially arranging representative network nodes on a 2D grid. This transformation decouples the nodes as images, enabling the use of convolutional neural networks (CNNs) with global receptive fields and multi-scale pyramids, thus overcoming limitations of existing biological network analysis methods in scalability, memory efficiency, and long-range context capture. Graph2Image also facilitates seamless integration with other imaging and omics modalities and enhances interpretability through direct visualization of node-associated images. When applied to several large-scale biological network datasets, Graph2Image improved classification accuracy by up to 67.2% over existing methods and provided interpretable visualizations that revealed biologically coherent patterns. It also allows analysis of very large biological networks (nodes > 1 billion) on a personal computer. Graph2Image thus provides a scalable, interpretable, and multimodal-ready approach for biological network analysis, offering new opportunities for disease diagnosis and the study of complex biological systems.

cs.LG↗