Tuo Wang

Boyu Yuan, Jiamiao Lu, Weichuan Zhang et al.

This study introduces an automated deep learning framework for predicting brain injury (BI) in preterm infants from T2-weighted MRI (dHCP dataset). We propose GloResNet, a lightweight 3D CNN based on ResNet-10, pretrained on MedicalNet to address data scarcity. A global manifold mapping strategy first resamples each 3D volume to 128x128x128 and then applies subject-wise z-score intensity normalization, thereby preserving global topology while standardizing appearance. Training integrates mixup, class weighting, and test-time augmentation for robustness. In 5-fold cross-validation, GloResNet achieved 75.18% average accuracy (peak 81.82%), with specificity 0.81 and sensitivity 0.76. Results demonstrate that a topology-aware lightweight CNN has the capability to effectively predict neonatal BI, offering a non-invasive screening tool. The source code of this paper can be obtained from the GitHub repository: https://github.com/ICL-SUST/GloResNet-Preterm-Brain

Linyue Zhang, Wenyi Zeng, Zicheng Pan et al.

Feature reconstruction techniques are widely applied for few-shot fine-grained image classification (FSFGIC). Our research indicates that one of the main challenges facing existing feature-based FSFGIC methods is how to choose the size of the receptive field to extract feature descriptors (including spatial and frequency feature descriptors) from different category input images, thereby better performing the FSFGIC tasks. To address this, an adaptive receptive field-based spatial-frequency feature reconstruction network (ARF-SFR-Net) is proposed. The designed ARF-SFR-Net has the capability to adaptively determine receptive field sizes for obtaining spatial and frequency features, and effectively fuse them for reconstruction and FSFGIC tasks. The designed ARF-SFR-Net can be easily embedded into a given episodic training mechanism for end-to-end training from scratch. Extensive experiments on multiple FSFGIC benchmarks demonstrate the effectiveness and superiority of the proposed ARF-SFR-Net over state-of-the-art approaches. The code is available at: https://github.com/ICL-SUST/ARF-SFR-Net.git.

Tuo Wang, Adithya Kulkarni, Tyler Cody et al.

Uncertainty estimation is essential for enhancing the reliability of Large Language Models (LLMs), particularly in high-stakes applications. Existing methods often overlook semantic dependencies, relying on token-level probability measures that fail to capture structural relationships within the generated text. We propose GENUINE: Graph ENhanced mUlti-level uncertaINty Estimation for Large Language Models, a structure-aware framework that leverages dependency parse trees and hierarchical graph pooling to refine uncertainty quantification. By incorporating supervised learning, GENUINE effectively models semantic and structural relationships, improving confidence assessments. Extensive experiments across NLP tasks show that GENUINE achieves up to 29% higher AUROC than semantic entropy-based approaches and reduces calibration errors by over 15%, demonstrating the effectiveness of graph-based uncertainty modeling. The code is available at https://github.com/ODYSSEYWT/GUQ.

Tuo Wang, Jian Kang, Yujun Yan et al.

Conformal prediction for graph neural networks (GNNs) offers a promising framework for quantifying uncertainty, enhancing GNN reliability in high-stakes applications. However, existing methods predominantly focus on static graphs, neglecting the evolving nature of real-world graphs. Temporal dependencies in graph structure, node attributes, and ground truth labels violate the fundamental exchangeability assumption of standard conformal prediction methods, limiting their applicability. To address these challenges, in this paper, we introduce NCPNET, a novel end-to-end conformal prediction framework tailored for temporal graphs. Our approach extends conformal prediction to dynamic settings, mitigating statistical coverage violations induced by temporal dependencies. To achieve this, we propose a diffusion-based non-conformity score that captures both topological and temporal uncertainties within evolving networks. Additionally, we develop an efficiency-aware optimization algorithm that improves the conformal prediction process, enhancing computational efficiency and reducing coverage violations. Extensive experiments on diverse real-world temporal graphs, including WIKI, REDDIT, DBLP, and IBM Anti-Money Laundering dataset, demonstrate NCPNET's capability to ensure guaranteed coverage in temporal graphs, achieving up to a 31% reduction in prediction set size on the WIKI dataset, significantly improving efficiency compared to state-of-the-art methods. Our data and code are available at https://github.com/ODYSSEYWT/NCPNET.

Bowen Xu, Xinyue Zeng, Jiazhen Hu et al.

Building trustworthy clinical AI systems requires not only accurate predictions but also transparent, biologically grounded explanations. We present \texttt{DiagnoLLM}, a hybrid framework that integrates Bayesian deconvolution, eQTL-guided deep learning, and LLM-based narrative generation for interpretable disease diagnosis. DiagnoLLM begins with GP-unmix, a Gaussian Process-based hierarchical model that infers cell-type-specific gene expression profiles from bulk and single-cell RNA-seq data while modeling biological uncertainty. These features, combined with regulatory priors from eQTL analysis, power a neural classifier that achieves high predictive performance in Alzheimer's Disease (AD) detection (88.0\% accuracy). To support human understanding and trust, we introduce an LLM-based reasoning module that translates model outputs into audience-specific diagnostic reports, grounded in clinical features, attribution signals, and domain knowledge. Human evaluations confirm that these reports are accurate, actionable, and appropriately tailored for both physicians and patients. Our findings show that LLMs, when deployed as post-hoc reasoners rather than end-to-end predictors, can serve as effective communicators within hybrid diagnostic pipelines.

Xinyue Zeng, Tuo Wang, Adithya Kulkarni et al.

Recent advances in protein structure prediction have achieved near-atomic accuracy for well-folded proteins. However, current benchmarks inadequately assess model performance in biologically challenging contexts, especially those involving intrinsically disordered regions (IDRs), limiting their utility in applications such as drug discovery, disease variant interpretation, and protein interface design. We introduce DisProtBench, a comprehensive benchmark for evaluating protein structure prediction models (PSPMs) under structural disorder and complex biological conditions. DisProtBench spans three key axes: (1) Data complexity, covering disordered regions, G protein-coupled receptor (GPCR) ligand pairs, and multimeric complexes; (2) Task diversity, benchmarking twelve leading PSPMs across structure-based tasks with unified classification, regression, and interface metrics; and (3) Interpretability, via the DisProtBench Portal, which provides precomputed 3D structures and visual error analyses. Our results reveal significant variability in model robustness under disorder, with low-confidence regions linked to functional prediction failures. Notably, global accuracy metrics often fail to predict task performance in disordered settings, emphasizing the need for function-aware evaluation. DisProtBench establishes a reproducible, extensible, and biologically grounded framework for assessing next-generation PSPMs in realistic biomedical scenarios.