Cholangiocarcinoma

Background: Microvascular invasion (MVI) predicts recurrence and survival in hepatocellular carcinoma (HCC) but requires postoperative histopathology for diagnosis. We developed and validated a model integrating multimodal ultrasound and clinical data for preoperative MVI prediction. Methods: This multicenter study included 489 patients with HCC from eight centers. All patients had B-mode ultrasound (BUS), color Doppler flow imaging (CDFI), dynamic contrast-enhanced ultrasound (DCE-US), and clinical information. Data from seven centers (n = 421) were used for model development with five-fold cross-validation; data from the remaining center (n = 68) formed an independent external validation cohort. The proposed multimodal information fusion network used modality-specific encoders, a hemodynamic temporal change module for bidirectional DCE-US perfusion changes, and a representation consistency learning module to align heterogeneous ultrasound representations before Transformer-based fusion. Results: In external validation, DCE-US achieved the highest single-modality area under the receiver operating characteristic curve (AUC; 0.8545+/-0.0198), versus clinical information (0.6715+/-0.0156), CDFI (0.6435+/-0.0344), and BUS (0.6087+/-0.0417). Pixel-difference sampling and the proposed temporal module outperformed alternative sampling and video representation methods. The full model achieved the best performance, with an AUC of 0.8953+/-0.0180, accuracy of 81.18%+/-2.83%, sensitivity of 86.40%+/-6.69%, and specificity of 78.14%+/-6.28. Conclusions: Integrating multimodal ultrasound and clinical information enabled promising preoperative MVI prediction in HCC. DCE-US was the main source of predictive information, while BUS, CDFI, and clinical information provided complementary value. The proposed framework may support preoperative risk stratification and individualized clinical decision-making.

This study explores the use of deep learning and explainable artificial intelligence to diagnose hepatocellular carcinoma (HCC) and define effective biomarkers across five different stages of disease development using a transcriptomic biomarker HCC dataset constructed via semi-supervised learning from three source datasets. Several deep learning experiments were conducted with different feature extraction techniques and gene sets to identify the most effective features for training high-accuracy models with minimal loss. The best-performing model, using 15 selected genes with the SelectKBest algorithm, achieved 90.74% accuracy, while the model with the lowest recorded loss of 0.3187 was obtained using 20 selected genes. To address the issue of class imbalance in the dataset, a weighted training approach was conducted, and for model transparency and interpretability a SHAP-based XAI analysis provided insights into the model's decision-making, consistently finding DNAJB14 as the most influential gene. Functional validation in this study has provided compelling evidence that DNAJB14 plays an important role in the adverse properties of HCC and that its inhibition effectively reverses tumour cell migration, invasion, colony and sphere formation. The main limitation of this study is the dataset's class imbalance, and while weighted training helped mitigate this, further research and additional data are needed to guarantee model generalizability. Future studies should also explore the influence of genetic variations, environmental factors, and clinical differences on model performance across diverse populations.

Accurate segmentation of colorectal liver metastases (CRLM) in contrast-enhanced computed tomography (CT) is important for response assessment, surgical planning, and follow-up. We propose two parameter-efficient spectral adapters for the Segment Anything Model (SAM): the Directional Spectral Adapter (DiSECT) and Spectral Instance-Guided Adapter (SiGA). DiSECT uses singular value decomposition of frozen weights to constrain residual updates to leading spectral directions, while SiGA adds global and input-conditioned gating through a multilayer perceptron. We evaluate these methods on 446 contrast-enhanced CT volumes (355 training, 91 testing) and compare them with LoRA, QLoRA, convolutional adapters (CAD), and a 3D nnU-Net baseline. Experiments consider single-point, three-point, bounding-box, and no-prompt regimes. SiGA achieves the best single-point performance with a Dice score of 0.77, IoU of 0.69, and HD95 of 35.39 mm. Under no-prompt inference, SiGA reaches 0.76 Dice, 0.68 IoU, and 46.76 mm HD95, comparable to the nnU-Net baseline (0.758 Dice). DiSECT uses only 0.14 million trainable parameters. These results show that spectral adapters can efficiently adapt SAM for CRLM segmentation while retaining strong accuracy with limited trainable parameters.

Adapting natural-image foundation models like DINOv3 to multi-modal medical imaging is challenging due to the significant domain gap between natural color images and multi-channel medical scans. We present a unified, patch-based framework that processes raw multimodal imaging through training-free registration, automated localization, and mask-filtered patch extraction. This architecture culminates in a hierarchical strategy that aggregates patch-level insights into subject-level diagnostics. Using liver fibrosis staging as a case study, we evaluate four patch-level feature representations: handcrafted Radiomics features, learned ResNet features, pre-trained foundation model SAM-Med2D features, and frozen DINOv3 features. To ensure a controlled comparison, all models utilize the same lightweight MLP head and are evaluated across both rigid and deformable registration settings. Our training protocol focuses on mild fibrosis (S1) and cirrhosis (S4) classes only, enabling a single classifier to address both substantial fibrosis detection and cirrhosis staging. Evaluated via 10 random train (90%)/ test (10%) splits on 360 subjects from the CARE 2025 Liver Track 4 cohort, our DINOv3-based framework significantly outperforms all baselines, achieving the best classification accuracy of 78.4% for S1 and 75.8% for S4.

Preoperative prediction of perineural invasion (PNI) in cholangiocarcinoma (CCA) is clinically valuable but remains challenging because PNI-related cues on magnetic resonance imaging (MRI) are subtle, sparse, and spatially localized around the tumor boundary. Standard 3D CNN and transformer architectures process volumetric data in a dense or spatially uniform manner, which can dilute subtle PNI-related evidence while requiring a large number of multiply-accumulate operations over 3D feature grids. To address these limitations, we propose SCINTILLA-SNN, a 3D spiking network composed of a four-stage hierarchical backbone and a Multi-Scale Spike Aggregation (MSSA) module for PNI prediction. The backbone extracts hierarchical volumetric representations through spiking convolutional stages and local spike window modulation stages. Given the resulting stage-wise representations, MSSA maps each spatial token to a learnable content value and modulates it with a spike-dynamics gate derived from firing rate and timestep-wise membrane-potential variability. The resulting score, referred to as the diagnostic token score, is used to selectively aggregate sparse PNI-related evidence. Experiments on a 10-year retrospective cohort of 182 CCA patients show that SCINTILLA-SNN achieves an AUROC of 0.748 under 5-fold cross-validation, while reducing the estimated inference energy by 23.18$\times$ compared with dense MAC-only computation of the same network.

Perineural invasion (PNI) is an adverse histopathologic marker in intrahepatic cholangiocarcinoma (ICC), but it is usually confirmed only after resection. Preoperative T2-weighted MRI may provide noninvasive imaging cues predictive of PNI, although labels are available only at the patient level without slice- or voxel-level annotations. We propose Order-Aware Slab Multiple Instance Learning (OAS-MIL), a weakly supervised framework for patient-level PNI prediction. Each tumor-centered MRI crop is represented as an ordered sequence of overlapping 2.5D slabs formed from contiguous axial slices. A shared encoder extracts slab-level features, which are aggregated by a permutation-invariant set-attention branch and a bidirectional sequence-attention branch. Using five-fold label-stratified cross-validation at the patient level, OAS-MIL achieved a mean AUROC of 0.770, outperforming the evaluated volumetric and MIL baselines. These results suggest that axial order provides a useful inductive bias for weakly supervised PNI prediction from MRI.

Microwave ablation (MWA) is a promising minimally invasive treatment for liver tumors, but its therapeutic outcome strongly depends on patient-specific planning of antenna insertion trajectory, power, and treatment duration. Accurate numerical simulation can provide physically reliable ablation predictions; however, its high computational cost limits its use in optimization-based planning, where repeated forward evaluations are required. To address this issue, we propose a digital twin-based automatic planning framework that combines a neural ablation prediction model with a genetic algorithm. The model was trained on multiphysics simulation data generated from patient-specific tumor and vessel structures, antenna configurations, and treatment conditions, and was used as a fast forward model during planning. The prediction model achieved a Dice score of 95.1%, enabling accurate deep learning-based optimization. In 13 unseen planning cases, the proposed method improved ablation efficiency by 54.3% and reduced organ damage by 55.0% compared with clinician-defined planning, while slightly shortening the insertion path length by 3.3%. Most generated plans were also judged clinically applicable by MWA specialists. Furthermore, the framework enabled approximately 420-fold faster planning than numerical-simulation-based planning, demonstrating its potential as a fast digital twin for quantitative and personalized MWA treatment planning. The code is available at: https://github.com/SeonAengCho/MWA-Planning.git

Accurate 3D--2D liver registration, which aligns preoperative 3D models to partial, view-dependent intraoperative surface observations, is critical for AR-guided laparoscopic surgery but remains challenging due to severe occlusion, limited visibility, and the lack of 3D ground-truth supervision. Existing landmark-free approaches perform partial-to-complete geometric alignment, yet robust self-supervision under extreme partial visibility remains difficult. We propose Vis2Reg, a visibility-aware registration framework that explicitly constrains deformation using mask-consistent visible regions. We introduce a visibility-aware self-supervision that derives a visible-domain 3D supervision signal from intraoperative masks, enabled by differentiable point rasterization and mask-guided back-projection. This formulation improves robustness under severe occlusion while maintaining fully self-supervised learning. Vis2Reg combines a robust geometric rigid initialization module with an implicit neural deformation field for stable alignment. Vis2Reg achieves a Dice score of 92.6% and a Chamfer Distance of 1.43 mm on real intraoperative datasets, with 111 ms per-frame inference time, demonstrating both accuracy and practical efficiency.

Differentiating non-alcoholic steatohepatitis (NASH) from non-alcoholic fatty liver disease (NAFLD) using ultrasound remains challenging due to subtle tissue alterations and the limited information available in conventional B-mode imaging. In this work, we investigate whether complementary ultrasound representations derived from the same acquisition can improve NASH versus NAFLD classification. Specifically, we combine conventional B-mode ultrasound with physics-guided and local phase-based image representations and evaluate their effectiveness using self-supervised masked autoencoders (MAEs) and graph convolutional networks (GCNs). Experiments were conducted on a multi-site Mayo Clinic cohort consisting of 2,547 liver ultrasound scans from 125 patients. Compared with conventional B-mode ultrasound alone, complementary ultrasound representations consistently improved classification performance, yielding gains of up to 32.4% in accuracy and 91.2% in F1-score. Furthermore, performance improvements were consistently observed across age groups, sex, race, ethnicity,and acquisition sites.

Perineural invasion (PNI) is associated with poor postoperative outcomes in intrahepatic cholangiocarcinoma, but it is confirmed by surgical pathology. Existing preoperative imaging models often rely on radiologist-defined variables, contrast-enhanced imaging, or manual annotations. We propose an anatomy-privileged teacher--student framework for patient-level PNI prediction from T2-weighted MRI. During training, the teacher uses MRI with tumor and liver masks to learn dense token routing, and the student distills this guidance to retain and aggregate informative tokens under a fixed budget. Anatomical supervision is restricted to training, and the deployed model does not require masks at inference. In 155 patients, the proposed method achieved the highest mean AUROC of 0.750 among matched MRI-only baselines evaluated under the same protocol, with 1.43 GFLOPs and 8.02 ms per case on a Jetson Orin Nano Super Developer Kit.

Perineural invasion (PNI) is associated with poor prognosis in cholangiocarcinoma (CCA). However, its detection from 3D MRI remains challenging due to the subtle and spatially heterogeneous imaging signatures at the tumor periphery. Capturing such spatially sparse cues necessitates volumetric analysis of 3D MRI, but existing deep learning approaches incur prohibitive computational costs on volumetric medical images, limiting their clinical deployment. We propose Dual Sparsity Spikformer (SpikeDS), a spiking neural network architecture that jointly exploits activation sparsity from binary spike communication and spatial sparsity from window pruning based on firing rates. SpikeDS introduces Dual Sparsity Spiking Attention (DSSA), which combines two complementary mechanisms. The first is Window-based Expert Mixture Spiking Attention (W-EMSA), which selectively applies attention only to salient windows identified by their firing rates. The second is Cross-Window Spiking Self-Attention (CW-SSA), which enables global context exchange through an asymmetric scheme in which pruned windows still contribute as key-value sources. Evaluated on a clinical cohort of 139 CCA patients via 5-fold cross-validation, SpikeDS achieves an AUC of 0.753 while consuming only 14.4 mJ, surpassing the best baseline in both AUC and energy efficiency. These results suggest that dual sparsity provides an effective hardware-aware strategy for improving the efficiency of 3D spiking transformers without compromising diagnostic performance.

Perineural invasion (PNI) is a critical prognostic factor in cholangiocarcinoma. However, its preoperative prediction from magnetic resonance imaging (MRI) remains challenging due to subtle imaging features that extend beyond tumor boundaries into surrounding regions. Conventional convolutional neural networks are limited in capturing long-range spatial dependencies. Transformer-based architectures improve global modeling of volumetric MRI by aggregating spatially distributed contextual cues, yet capturing subtle and noise-sensitive patterns in peritumoral regions remains challenging. Diffusion-based classifiers offer an alternative formulation by leveraging denoising-based class scoring to better capture such subtle patterns. However, these approaches introduce substantial computational overhead due to the combination of transformer-based modeling and iterative denoising processes. To address these challenges, we formulate PNI prediction as a diffusion-based classification problem and implement the denoising network using a transformer-based representation. To improve computational efficiency, we introduce adaptive routing across attention heads, spatial tokens, and MLP width. Experimental results demonstrate that the proposed approach achieves an AUC of 0.731 with 257.57 GFLOPs.

Perineural invasion (PNI) is a critical prognostic factor in cholangiocarcinoma. Non-invasive prediction from 3D MRI is challenging, demanding models that efficiently capture both fine-grained details and global context. We propose the Multi-window Mixture-of-Head Attention Transformer (MMA-Former), a novel end-to-end 3D architecture featuring a Coarse-Fine Transformer (CFT) structure for parallel multi-scale feature extraction. We advance this structure by integrating a novel Window-Specific Mixture-of-Head attention (WS-MoH) mechanism. Unlike standard Multi-Head Self Attention (MSA), WS-MoH generates a representation for each 3D window and dynamically routes the entire window to specialized or common attention heads. This enables spatially adaptive feature extraction tailored to the local context of each window, enhancing specialization and reducing redundancy without increasing parameters. Evaluated on a retrospective dataset of 168 T1-weighted MRI scans, MMA-Former achieved an AUC of 0.752, outperforming other 3D architectures, including the best CNN (AUC of 0.708) and Transformer baselines (AUC of 0.681).

Hepatocellular carcinoma (HCC) is a common malignancy and a leading cause of cancer-related mortality. Current guidelines and staging systems provide coarse categories, but often miss within-stage heterogeneity and the clinical context in electronic medical records (EMRs). We present HCC-STAR (Hepatocellular Carcinoma Staging, Treatment And pRognosis), a clinically aligned large language model that reads routine EMR narratives and jointly outputs risk score-based staging, ranked guideline-consistent treatments with evidence-based rationales, and individualized survival estimates. We curated about 30,000 HCC cases from SEER and expanded them into EMR-style narrative training data using a clinician-validated, prompt-based augmentation workflow. On this corpus, we developed a knowledge-aligned reasoning framework optimized with a step-verifiable composite reward, moving beyond text-level memorization of clinical guidelines. In a multi-center cohort of 6,668 patients from 12 hospitals in China, HCC-STAR achieved state-of-the-art performance in treatment recommendation and risk stratification compared with clinical guidelines and competitive models, including GPT-5 and Gemini-2.5 Pro. Hypothetical overall-survival analysis showed a median survival of 51 months under adherence to HCC-STAR recommendations, compared with 29 and 32 months under BCLC and CNLC. In clinician-centric evaluations, blinded hepatobiliary specialists rated HCC-STAR's reasoning and evidence-based justifications as trustworthy. The model surpassed resident and attending physicians in treatment accuracy and helped physicians make more accurate decisions faster when used as an assistant. These findings support HCC-STAR as a reliable and verifiable decision-support system for risk stratification and precision therapy in HCC.

As hematoxylin & eosin (H&E) staining constitutes the primary entry point in routine diagnostic workflows, computer-aided diagnosis from whole-slide H&E images is of particular clinical relevance. However, substantial variability in specimen preparation, staining protocols, and scanning conditions, together with inherent uncertainty in expert pixel-level annotations, makes automated analysis of H&E-stained images challenging. In this study, we propose a semantic segmentation-based framework for image-level diagnosis, grounded in the clinically motivated assumption that each histopathological image corresponds to a single cancer type. Image-level predictions are obtained by assigning the class of the dominant pixel-level label in the segmentation output. To ensure clinical relevance, we adopt the nnU-Net architecture and train it on a publicly available dataset collected in our study with pixel-level annotations for three liver cancer types: hepatocellular cacrcinoma (HCC; 55 images from 30 patients), cholangiocellular carcinoma (CCA; 55 images from 29 patients), and colorectal metastatic adenocarcinoma (CMA; 60 images from 30 patients). Annotations were independently provided by four pathologist. We hypothesize that the combination of stain normalization and semantic segmentation mitigates domain shift and reduces sensitivity to annotation noise. Five-fold cross-validation yielded balanced accuracy of 0.975 (HCC), 0.950 (CCA), and 1.000 (CMA), comparable to results obtained with immunohosthochemical staining and superior to several deep learning models trained on patch-level annotations. The proposed framework has the potential to support pathologists in prioritizing immunohistochemical marker selection, thereby reducing diagnostic costs and turnaround time. Integration with immunohistochemical findings improve overall diagnostic reliability.

Hepatitis C is a liver infection caused by a virus, which results in mild to severe inflammation of the liver. Over many years, hepatitis C gradually damages the liver, often leading to permanent scarring, known as cirrhosis. Patients sometimes have moderate or no symptoms of liver illness for decades before developing cirrhosis. Cirrhosis typically worsens to the point of liver failure. Patients with cirrhosis may also experience brain and nerve system damage, as well as gastrointestinal hemorrhage. Treatment for cirrhosis focuses on preventing further progression of the disease. Detecting cirrhosis earlier is therefore crucial for avoiding complications. Machine learning (ML) has been shown to be effective at providing precise and accurate information for use in diagnosing several diseases. Despite this, no studies have so far used ML to detect cirrhosis in patients with hepatitis C. This study obtained a dataset consisting of 28 attributes of 2038 Egyptian patients from the ML Repository of the University of California at Irvine. Four ML algorithms were trained on the dataset to diagnose cirrhosis in hepatitis C patients: a Random Forest, a Gradient Boosting Machine, an Extreme Gradient Boosting, and an Extra Trees model. The Extra Trees model outperformed the other models achieving an accuracy of 96.92%, a recall of 94.00%, a precision of 99.81%, and an area under the receiver operating characteristic curve of 96% using only 16 of the 28 features.

Non-alcoholic fatty liver disease (NAFLD) affects roughly 25% of global adults, posing substantial hepatic and cardiovascular risks. Yet, population-level screening tools remain inadequate. We present Method, a machine-learning framework for NAFLD risk prediction coupling gradient-boosted decision trees with conformal prediction to yield calibrated, distribution-free coverage guarantees on individual risk estimates. It integrates a mutual-information-based stability selection procedure to identify a compact, clinically interpretable feature subset via bootstrap resampling, constructing prediction sets whose marginal coverage provably exceeds a user-specified confidence level. We evaluated Method on a multicenter cohort from Guangzhou, China (primary n=2,187; external validation n=412) using 78 candidate features across demographics, metabolic biomarkers, and lifestyle factors. Method achieves an AUROC of 0.912 internally and 0.891 externally, outperforming deep neural networks, TabNet, support vector machines, and logistic regression. Conformal prediction sets achieve 91.3% empirical coverage at the 90% nominal level. A three-tier risk stratification derived from these scores separates the population into distinct groups, with the high-risk subgroup showing a 12-month progression rate 4.7 times that of the low-risk tier. The selected features -- notably waist circumference, ALT, GGT, triglycerides, fasting glucose, and BMI -- align with established metabolic risk factors, providing biological plausibility.

Histological scoring is essential for diagnosing Non-Alcoholic Fatty Liver Disease (NAFLD), yet its automation remains challenging due to the high annotation cost and negative transfer among the strongly correlated NAFLD Activity Score (NAS) indicators in multi-task learning. To address this issue, we propose a subspace-decoupled multi-task Vision Transformer (ViT) that integrates lightweight task-specific Adapters with orthogonality-based constraints. This design constructs independent feature subspaces for steatosis, ballooning, and inflammation, effectively reducing task interference while retaining shared representations. We further construct a curated multi-task mouse NAFLD histology dataset with expert annotations for all NAS components. Experimental results demonstrate that the proposed method improves multi-task stability and generalization with substantially reduced computational cost compared to training separate single-task models. The code and the curated dataset have been prepared and will be made publicly available upon acceptance to support reproducibility.

Hepatocellular carcinoma (HCC) is biologically heterogeneous, shaped by the interplay between hepatic functional reserve and tumor-related oncologic factors; thus, similar survival outcomes may reflect fundamentally different underlying biological processes. Prognostic modeling in HCC is informed by rich multimodal information from multiparametric MRI and radiology reports from routine clinical practice. Existing prognostic vision-language models (VLMs) learn a single entangled latent representation that blends hepatic and tumor-related factors, limiting both accuracy and biological interpretability. We present BioFact-MoE, a biologically factorized Mixture of Experts (MoE) framework that explicitly decomposes liver and tumor factors via biologically supervised experts within a residual MoE survival architecture. On a HCC cohort of N=588 patients (pretrained on 4,582 3D MRI image-report pairs), BioFact-MoE consistently improves survival prediction over all baselines across time horizons, achieving 12-, 18-, and 24-month AUCs of 75.33%, 75.85%, and 73.96%. Beyond scalar risk prediction, gated expert weights enable phenotype-aware risk stratification. Pathway-informed gating uncovers clinically meaningful treatment-associated survival heterogeneity. In held-out validation, hepatic and tumor embeddings show selective associations with liver function and tumor burden markers, respectively (p<0.05), without supervision. The code is available at https://github.com/jy-639/BioFact-MoE.

Despite years of methodological progress, how far AI has come in liver fibrosis staging has never been systematically evaluated under the heterogeneous, multi-center conditions that define clinical practice. To address this gap, we introduce LiFS, a large-scale dataset and benchmark derived from the MICCAI 2025 CARE-Liver challenge, comprising 610 patients across multiple centers and scanners with multi-sequence MRI. To the best of our knowledge, LiFS is the first benchmark providing complete gadoxetic acid-enhanced sequences with histopathology-confirmed annotations from diverse real-world scanners. Through systematic evaluation of 9 independently developed methods selected from 96 registered teams against in-cohort radiologist reference results, our findings address how far current AI has progressed toward clinical-level liver fibrosis staging from three complementary perspectives. First, against radiologists, the best AI methods were broadly comparable to the senior radiologist and significantly exceeded the junior radiologist in selected settings, while median AI performance generally approached junior-radiologist levels. Second, from a data perspective, cross-center heterogeneity, label imbalance, and contrast-enhanced sequence variability emerge as the dominant challenges for AI methods. Third, from a technical perspective, methodological design choices, including spatial registration, input dimensionality, multi-modal fusion strategy, and backbone architecture, appear to modulate cross-center robustness, although no single choice alone closes the gap. Overall, LiFS provides a rigorous real-world benchmark for positioning the current state of AI in liver fibrosis staging and for enabling future research on the key challenges that limit clinically reliable deployment.

Advanced fibrosis is a major determinant of liver-related morbidity in metabolic dysfunction-associated steatotic liver disease (MASLD). FIB-4 is widely used as a first-line non-invasive test, but its fixed formula may underuse diagnostic information contained in age, aspartate aminotransferase, alanine aminotransferase, and platelet count. We evaluated whether machine-learning-enhanced non-invasive testing (MLE-NIT) can improve advanced fibrosis detection while preserving this FIB-4 variable space. We used three biopsy-confirmed MASLD cohorts from China, Malaysia, and India (n=784). The Chinese cohort was split into 486 training and 54 internal validation/tuning patients; final performance was reported only on the Malaysian and Indian external cohorts. Models used five variables: age, FIB-4, aspartate aminotransferase, platelet count, and alanine aminotransferase. We compared FIB-4 with a shallow-deep neural network (s-DNN), TabPFN, and gpt-4o-2024-08-06. FIB-4 achieved external ROC-AUCs of 0.75 and 0.60 in Malaysia and India, respectively. TabPFN achieved 0.69 and 0.66, fine-tuned GPT-4o achieved 0.75 and 0.63, and the s-DNN achieved 0.77 and 0.67, respectively. The s-DNN contained only 354 trainable parameters, compared with 7,244,554 for TabPFN, yet provided a more balanced external operating profile. Calibration showed s-DNN Brier scores of 0.18 and 0.22, and permutation importance identified AST and FIB-4 as dominant variables. Compact non-linear MLE-NITs may enhance FIB-4-based fibrosis assessment without increasing clinical data requirements.

Non-alcoholic fatty pancreas disease (NAFPD) is an underdiagnosed condition associated with metabolic syndrome, insulin resistance, and increased risk of pancreatic cancer. Diagnosis typically relies on subjective visual assessment of ultrasound images by clinicians. We propose an end-to-end framework for automatically classifying normal versus fatty pancreas from abdominal ultrasound images. Our method employs a TransUNet-based segmentation architecture with a ResNet encoder and transformer bottleneck to delineate the pancreas and the splenic vein, followed by anatomically-guided patch extraction and patient-level classification through pairwise texture comparison. The feature engineering mimics clinical reasoning by comparing the echogenicity of peri-venous fat to the pancreatic parenchyma, providing an interpretable signal for classification. The segmentation models are initialized via domain-specific transfer learning from a liver segmentation task. We validate the full pipeline on a clinical dataset of 214 abdominal ultrasound images with 107 expert-labeled cases using 5-fold cross-validation. SVM with RBF kernel achieves a mean cross-validated accuracy of 89.7%,$\pm$,1.8% and F1 of 0.898,$\pm$,0.019, while the unsupervised K-Means baseline reaches 87.8% accuracy, demonstrating that the proposed features capture the relevant clinical signal even without labeled training data. To our knowledge, this is the first end-to-end automated framework for fatty pancreas classification from ultrasound using segmentation-guided texture analysis.

Liver cirrhosis is a major global health problem causing millions of deaths annually, and timely detection with aggressive treatment can significantly improve patients' quality of life. Modelling complex diseases from biomedical data is computationally challenging due to high dimensionality, strong feature correlations, noise, and limited labelled samples. Conventional Machine Learning (ML) pipelines often struggle with robustness, interpretability, and generalisation under such conditions. In this study, we propose an ML-driven multi-stage decision framework for complex disease modelling and therapeutic exploration. The framework integrates single-cell transcriptomic profiling, high-dimensional network-based feature stabilisation, multi-model learning, deep representation construction, and post-hoc decision support. Specifically, single-cell sequencing data were analysed to identify key cellular subpopulations, followed by high-dimensional weighted gene co-expression network analysis (hdWGCNA) to stabilise gene modules under sparsity and noise. To enhance non-linear feature interaction modelling, tabular molecular features were restructured into two-dimensional disease maps and analysed using a CNN. Finally, molecular docking was incorporated as a decision-support module to evaluate candidate therapeutic compounds. Using liver cirrhosis as a representative case, the framework identified a disease-associated endothelial subpopulation and extracted seven robust signature genes (HSPB1, GADD45A, CLDN5, ATP1B3, C1QBP, ENPP2, and PARL). The CNN-based representation learning module outperformed conventional pipelines in classification. The framework is disease-agnostic and readily extends to other omics-driven biomedical applications involving uncertainty, heterogeneity, and limited samples.

Liver cancer, especially hepatocellular carcinoma (HCC), imposes a substantial global disease burden. Accurate diagnosis and prognostic assessment directly influence treatment selection and patient survival, and pathological examination remains the gold standard for liver cancer diagnosis. Identifying diverse tissue components and pathological subtypes on histopathology slides is crucial for estimating postoperative recurrence risk and overall prognosis. However, most publicly available resources are still provided at the whole-slide image (WSI) level, and well-annotated datasets for fine-grained tissue component identification in liver cancer are scarce, which hinders reproducible model development and the deployment of quantitative analysis tools. To address this gap, we release HepatoBench, a patch-level image database for liver cancer with annotations for seven key tissue categories. Based on HepatoBench, we train and open-source a deep learning classification model as a tissue recognition tool. Furthermore, we train a WSI-level tumor/non-tumor segmentation model to automatically localize lesion regions across entire slides. By integrating the patch-level tissue classifier with the WSI-level segmentation model, we build HepatoQuant, an end-to-end, disease-specific regional quantification tool for liver cancer, enabling a unified workflow from WSIs to tissue composition parsing and quantitative statistics. We also open-source HepatoBench, the benchmarking protocol, and supporting tools, providing a solid foundation for automated regional quantification and fair method comparison in liver cancer pathology.