Computer Methods and Programs in Biomedicine

Article	Citations
Identifying the patient harms to include in an in silico clinical trial	640
Real-time soft body dissection simulation with parallelized graph-based shape matching on GPU	377
Editorial Board	315
4-dimensional local radial basis function interpolation of large, uniformly spaced datasets	274
MSigSeg: An R package for multiple signals segmentation	223
Prediction of neoadjuvant therapy response to HER2-positive and triple-negative breast cancer: a multicenter proof-of-concept study	175
VesselKnife – software for the analysis of tubular structures in biomedical images	168
Importance of the enhanced cooling system for more spherical ablation zones: Numerical simulation, ex vivo and in vivo validation	138
VOC-DL: Deep learning prediction model for COVID-19 based on VOC virus variants	121
Influence of genetic mutations to atria vulnerability to atrial fibrillation: An in-silico 3D human atria study	117
Integrative analysis of RNA modification-related gene PUS7 in diagnosis, prognosis, and tumor microenvironment of hepatocellular carcinoma	110
A temporal convolutional network-based approach and a benchmark dataset for colonoscopy video temporal segmentation	107
An automatic pipeline for atlas-based fetal and neonatal brain segmentation and analysis	106
SC-Net: Symmetrical conical network for colorectal pathology image segmentation	105
A cloud-based consultation and collaboration system for radiotherapy: Remote decision support services for community radiotherapy centers	102
Modelling lower-limb peripheral arterial disease using clinically available datasets: impact of inflow boundary conditions on hemodynamic indices for restenosis prediction	100
CAPNet: Context attention pyramid network for computer-aided detection of microcalcification clusters in digital breast tomosynthesis	97
A Graph-guided Hybrid Regularization Method For Bioluminescence Tomography	96
MBGA-Net: A multi-branch graph adaptive network for individualized motor imagery EEG classification	93
Optimal machine learning methods for prediction of high-flow nasal cannula outcomes using image features from electrical impedance tomography	90
CUAMT: A MRI semi-supervised medical image segmentation framework based on contextual information and mixed uncertainty	90
Using machine learning models for predicting monthly iPTH levels in hemodialysis patients	84
TiDE-Net: A time-guided dual-encoder ResUNet for Positron Emission Tomography (PET) image denoising	83
In silico modeling of transcatheter heart valve oversizing and ellipticity, Part I: Establishing credibility of an advanced model	82
IML-UNet: A brain-inspired spatiotemporal collaborative encoding method for medical image sequence registration	82

Finite element analysis of conductive hearing loss caused by fixation and detachment of ligament and tendon in the middle ear	81
FMCW radar based high-precision gridless non-contact vital signs monitoring for Internet of Medical Things	76
Evaluation of deep learning training strategies for the classification of bone marrow cell images	76
Lung nodule classification using radiomics model trained on degraded SDCT images	76
Unsupervised band selection of medical hyperspectral images guided by data gravitation and weak correlation	74
MRI-based CFD simulations of transient blood flow in compliant aortas using the LDDMM framework	73
Unsupervised domain adaptation for nuclei segmentation: Adapting from hematoxylin & eosin stained slides to immunohistochemistry stained slides using a curriculum approach	72
An ensemble classifier for emotion classification from EEG and GSR signals for autism detection	72
MEFA-Unet: Multi-scale feature extraction and fusion attentional unet for segmenting short process of incus in otologic microsurgical scenarios	69
Oblique lateral interbody fusion: role of the elastic modulus of the cage material in mechanically induced osteogenesis	68
A real-time computer-aided diagnosis method for hydatidiform mole recognition using deep neural network	67
Temporal convolutional neural network-based feature extraction and asynchronous channel information fusion method for heart abnormality detection in phonocardiograms	66
Modelling of cardiac biventricular electromechanics with coronary blood flow to investigate the influence of coronary arterial motion on coronary haemodynamic	65
Light&fast generative adversarial network for high-fidelity CT image synthesis of liver tumor	65
An interactive and realistic phantom for cricothyroidotomy simulation of a patient with obesity through a reusable design using 3D-printing and Arduino	64
Cuffless blood pressure estimation using chaotic features of photoplethysmograms and parallel convolutional neural network	64
IODeep: An IOD for the introduction of deep learning in the DICOM standard	64
Detecting optimal biomarkers in ovarian cancer cells from high-dimensional mRNA expression data using machine learning	63
Fear of falling in community-dwelling older adults: What their gait acceleration pattern reveals	62
A study on brain tumor dynamics in two-dimensional irregular domain with variable-order time-fractional derivative	61
CTGAN-driven synthetic data generation: A multidisciplinary, expert-guided approach (TIMA)	61
SIMUS3: An open-source simulator for 3-D ultrasound imaging	59
Raw photoplethysmogram waveforms versus peak-to-peak intervals for machine learning detection of atrial fibrillation: Does waveform matter?	59
Multimodal radiomics based on lesion connectome predicts stroke prognosis	58
From local counterfactuals to global feature importance: efficient, robust, and model-agnostic explanations for brain connectivity networks	58
The impact of small movements with dual lumen cannulae during venovenous extracorporeal membrane oxygenation: A computational fluid dynamics analysis	58
Dual-modeling computational framework of magnetoelectric core-shell nanoparticles and nanochain for wireless peripheral nerve regeneration	57
Medical image super-resolution reconstruction algorithms based on deep learning: A survey	56
CPSS: Fusing consistency regularization and pseudo-labeling techniques for semi-supervised deep cardiovascular disease detection using all unlabeled electrocardiograms	56
S-Net: A novel shallow network for enhanced detail retention in medical image segmentation	55
A computational method to predict cerebral perfusion flow after endovascular treatment based on invasive pressure and resistance	54
Multi-electrode catheter PFA: Computational modeling and in vivo validation of lesion dynamics under energy-dose variants	53
Simulation-driven optimization of insulin therapy profiles in a commercial hybrid closed-loop system	53
TransAnno-Net: A Deep Learning Framework for Accurate Cell Type Annotation of Mouse Lung Tissue Using Self-supervised Pretraining	53
A myocardial reorientation method based on feature point detection for quantitative analysis of PET myocardial perfusion imaging	53
Retinex-qDPC: Automatic background-rectified quantitative differential phase contrast imaging	53
A numerical simulation study of soft tissue resection for low-damage precision cancer surgery	53
Editorial Board	52
Molecular dynamics simulation of hyaluronic acid hydrogels: Effect of water content on mechanical and tribological properties	52
Editorial Board	52
A multiconsistent computational methodology to resolve a diffusive epidemiological system with effects of migration, vaccination and quarantine	51
Prediction of iliac limb occlusion after endovascular aneurysm repair for abdominal aortic aneurysm by anatomical and near-wall hemodynamic characteristics combining numerical simulation and in vitro	51
CRMIPred: Identifying the spatial interactions among cis-regulatory modules via considering their cross-attended epigenetic profiles	51
Recurrence quantification analysis of rs-fMRI data: A method to detect subtle changes in the TgF344-AD rat model	51
A new computational pipeline for multicompartment modeling of liver perfusion	50
Phys-DAT: A physiologically-based pharmacokinetic model for unraveling the dissolution, transit and absorption processes using PhysPK®	49
Modified Theoretical Model Predicts Radial Support Capacity of Polymer Braided Stents	49
Automatic registration of dental CT and 3D scanned model using deep split jaw and surface curvature	49
A neural network framework for immediate temperature prediction of surgical hand-held drilling	47
Corrigendum to “Generation of post-meal insulin correction boluses in type 1 diabetes simulation models for in-silico clinical trials: More realistic scenarios obtained using a decision tree approach”	46

Regularized multi-task learning with individual-feature-based task correlations for Alzheimer’s cognitive score prediction	46
Corrigendum to “Segmentation of skin layers on HFUS images using the attention mechanism”, [Computer Methods and Programs in Biomedicine, 263 (2025) 108668]	45
Dynamic elastic modulus assessment of the early degeneration model of an intervertebral disc in cynomolgus monkeys with one strike loading	45
Multicentric intelligent cardiotocography signal interpretation using deep semi-supervised domain adaptation via minimax entropy and domain invariance	45
Digital signal extraction approach for cardiotocography image	44
Corticosteroid sensitivity detection in sepsis patients using a personalized data mining approach: A clinical investigation	43
Predicting 6-minute walking test outcomes in patients with chronic obstructive pulmonary disease without physical performance measures	43
ML3CNet: Non-local means-assisted automatic framework for lung cancer subtypes classification using histopathological images	42
PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation	42
Facial expressions to identify post-stroke: A pilot study	42
TGMIL: A hybrid multi-instance learning model based on the Transformer and the Graph Attention Network for whole-slide images classification of renal cell carcinoma	41
Multi-scale dual-channel feature embedding decoder for biomedical image segmentation	41
KUB-UNet: Segmentation of Organs of Urinary System from a KUB X-ray Image	40
A novel MCF-Net: Multi-level context fusion network for 2D medical image segmentation	40
Exploring emotional climate recognition in peer conversations through bispectral features and affect dynamics	39
Multi-scale simulation of red blood cell trauma in large-scale high-shear flows after Norwood operation	39
Predicting the Risk of Type B Aortic Dissection Using Hemodynamic Parameters in Aortic Arches: A Comparative Study between Healthy and Repaired Aortas	39
Performance and limitations of a supervised deep learning approach for the histopathological Oxford Classification of glomeruli with IgA nephropathy	39
A simple agent-based hybrid model to simulate the biophysics of glioblastoma multiforme cells and the concomitant evolution of the oxygen field	39
Missing data imputation using utility-based regression and sampling approaches	39
Disease X epidemic control using a stochastic model and a deterministic approximation: Performance comparison with and without parameter uncertainties	38
Integrating prior knowledge with deep learning for optimized quality control in corneal images: A multicenter study	38
PregGAN: A prognosis prediction model for breast cancer based on conditional generative adversarial networks	38
Evaluation of the linear and nonlinear classifiers for distinguishing between healthy subjects and patients with valvular heart diseases based on electrocardiograms, seismocardiograms, and gyrocardiog	38
Haemosync: A synchronisation algorithm for multimodal haemodynamic signals	37
A probabilistic generative model to discover the treatments of coexisting diseases with missing data	37
United multi-task learning for abdominal contrast-enhanced CT synthesis through joint deformable registration	37
Extension of physical activity recognition with 3D CNN using encrypted multiple sensory data to federated learning based on multi-key homomorphic encryption	37
Self-supervised learning with self-distillation on COVID-19 medical image classification	36
Data-driven sleep structure deciphering based on cardiorespiratory signals	36
Effect of pulmonary regurgitation on cardiac functions based on a human bi-ventricle model	36
Localizing the seizure onset zone and predicting the surgery outcomes in patients with drug-resistant epilepsy: A new approach based on the causal network	36
Artificial intelligence model for tumoral clinical decision support systems	36
Three-dimensional oxygen maps of tumors in real time – Analysis in the context of active tumor vasculature	36
Detecting cardiovascular diseases using ECG scans and explainable artificial intelligence	36
Coronary artery disease severity and location detection using deep-mining-based magnetocardiography pattern features	36
A multi-task learning model with reinforcement optimization for ASD comorbidity discrimination	36
Morphology-, noise-, and resolution-robust ultrasound elasticity imaging with Fourier neural operator	36
An improved binary particle swarm optimization algorithm for clinical cancer biomarker identification in microarray data	36
Video-based computational analysis of spontaneous movements in preterm infants: A longitudinal neuromotor assessment	35
Rad4XCNN: A new agnostic method for post-hoc global explanation of CNN-derived features by means of Radiomics	35
Towards robust multimodal ultrasound classification for liver tumor diagnosis: A generative approach to modality missingness	35
SP-XTIN: A single projection grating-based X-ray tri-contrast imaging network	35
MEDUSA©: A novel Python-based software ecosystem to accelerate brain-computer interface and cognitive neuroscience research	35
Lesion attention guided neural network for contrast-enhanced mammography-based biomarker status prediction in breast cancer	35
SFTNet: A microexpression-based method for depression detection	35
NeuroDM: Decoding and visualizing human brain activity with EEG-guided diffusion model	34
An accurate and trustworthy deep learning approach for bladder tumor segmentation with uncertainty estimation	34
MM-CCNB: Essential protein prediction using MAX-MIN strategies and compartment of common neighboring approach	34
A Medical image segmentation model with auto-dynamic convolution and location attention mechanism	34
Neonatal EEG seizure detection using a new signal structural complexity measure based on matching pursuit decomposition with nonstationary dictionary	34
Multi-target reconstruction based on subspace decision optimization for bioluminescence tomography	34
Monte Carlo modeling of hepatic steatosis based on stereology and spatial distribution of fat droplets	34
A practical strategy for data assimilation of cerebral intra-aneurysmal flows using a variational method with boundary control of velocity	34
Enlarging the thermal coagulation volume during thermochemical ablation with alternating acid-base injection by shortening the injection interval: A computational study	34
Robust prediction of parameterized cardiovascular hemodynamics using deep operator networks with time normalization	33
Editorial Board	33
A joint evaluation method of dynamic spectrum extraction methods for non-invasive blood component measurement based on stability coefficient, data point adoption rate, and smoothness of the spectrum	33
Progression of blood-borne viruses through bloodstream: A comparative mathematical study	33
Automatic segmentation and CT-based deep learning radiomics nomogram for predicting overall survival in patients with small cell lung cancer: A multicenter cohort study	33
Editorial Board	33
Editorial Board	33
Tailored cancer therapy by magnetic nanoparticle hyperthermia: A virtual scenario simulation method	33
The role of AI for improved management of breast cancer: Enhanced diagnosis and health disparity mitigation	33
DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS	33
A novel endoscopic posterior cervical decompression and interbody fusion technique: Feasibility and biomechanical analysis	33
Parameter quantification for oxygen transport in the human brain	33
A Multi-physics model of flow from coronary angiography: Insights to microvascular function	33
CAD-RADS scoring of coronary CT angiography with Multi-Axis Vision Transformer: A clinically-inspired deep learning pipeline	32
Recent advancements and future directions in automatic swallowing analysis via videofluoroscopy: A review	32
From free‐text electronic health records to structured cohorts: Onconum, an innovative methodology for real‐world data mining in breast cancer	32
Nonlinear dose-response relationship in tDCS-induced brain network synchrony: A resting-state whole-brain model analysis	32
A high-fidelity geometric multiscale hemodynamic model for predicting myocardial ischemia	32
A robust myoelectric pattern recognition framework based on individual motor unit activities against electrode array shifts	32
Surgical procedure prediction using medical ontological information	32
An end-to-end framework for intima media measurement and atherosclerotic plaque detection in the carotid artery	31
EESCN: A novel spiking neural network method for EEG-based emotion recognition	31
A novel fine-tuning and evaluation methodology for large language models on IoT raw data summaries (LLM-RawDMeth): A joint perspective in diabetes care	31
mvLognCorrEst: an R package for sampling from multivariate lognormal distributions and estimating correlations from uncomplete correlation matrix	31
Light scattering imaging modal expansion cytometry for label-free single-cell analysis with deep learning	31

Integrating multimodal data and deep learning for functional assessment and rehabilitation prediction after cerebral hemorrhage	31
Numerical study on optimization of quantitative treatment conditions for skin cancer photothermal therapy considering multiple blood vessels	31
Characterization of mechanical properties of adult chests during pre-hospital manual chest compressions through a simple viscoelastic model	31
Image-based Artificial Intelligence models in the diagnosis and classification of vascular anomalies of the soft tissue in the head and neck	31
Sensitivity analysis of paediatric knee kinematics to the graft surgical parameters during anterior cruciate ligament reconstruction: A sequentially linked neuromusculoskeletal-finite element analysis	31
Effect of a reduced arterial axial pre-stretch ratio during aging on the cardiac output and cerebral blood flow in the healthy elders	30
The synergy of cybernetical intelligence with medical image analysis for deep medicine: A methodological perspective	30
A risk and credibility framework for in silico clinical trials of medical devices	30
BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies	30
An agent-based model to assess large-scale COVID-19 vaccination campaigns for the Italian territory: The case study of Lombardy region	30
Dynamic simulation and analysis of the influence of urethral morphological changes on urodynamics after benign prostatic hyperplasia surgery: A computational fluid dynamics study	30
A deep dive into the static force transmission of the human masticatory system and its biomechanical effects on the temporomandibular joint	30
Human-computer interaction on virtual reality-based training system for vascular interventional surgery	30
Assessing ChatGPT's ability to emulate human reviewers in scientific research: A descriptive and qualitative approach	30
Automating COVID-19 epidemiological situation reports based on multiple data sources, the Netherlands, 2020 to 2023	30
Influence of adaptive denoising on Diffusion Kurtosis Imaging at 3T and 7T	29
High-order mesoscale modeling with geometrically conforming gray/white matter interface for traumatic brain injury	29
BGCSL: An unsupervised framework reveals the underlying structure of large-scale whole-brain functional connectivity networks	29
BaroWavelet: An R-based tool for dynamic baroreflex evaluation through wavelet analysis techniques	29
4D-Precise: Learning-based 3D motion estimation and high temporal resolution 4DCT reconstruction from treatment 2D+t X-ray projections	29
A SAS macro for multilevel Cosinor analysis	29
Shape-aware inference scheme for selective extraction of head-neck arteries on computer tomography angiography images	29
An expert review of the inverse problem in electrocardiographic imaging for the non-invasive identification of atrial fibrillation drivers	28
Patient-specific fluid-structure interaction modeling of cerebral aneurysm: influence of wall compliance, tissue prestress, and blood rheology	28
Real-time estimation of lung deformation from body surface using a general CoordConv CNN	28
Dual center validation of deep learning for automated multi-label segmentation of thoracic anatomy in bedside chest radiographs	28
Associative knowledge graphs for efficient sequence storage and retrieval	28
Towards open-set myoelectric gesture recognition via dual-perspective inconsistency learning	28
A real-time reconstructed grid method for soft tissue cutting and haptic	28
A Markov Chain methodology for care pathway mapping using health insurance data, a study case on pediatric TBI	28
Endoscopic versus laparoscopic bariatric procedures: A computational biomechanical study through a patient-specific approach	28
Physics-informed DynUNet for brain metastasis segmentation	28
Noninvasive and fast method of calculation for instantaneous wave-free ratio based on haemodynamics and deep learning	28
Automated quantitative analysis of peri-articular bone microarchitecture in HR-pQCT knee images	28
Computational simulation of cellular proliferation using a meshless method	28
Symbolic knowledge extraction for explainable nutritional recommenders	28
DE-MRI myocardial fibrosis segmentation and classification model based on multi-scale self-supervision and transformer	27
Scale resolving simulations of the effect of glottis motion and the laryngeal jet on flow dynamics during respiration	27
Chained occurrences of early afterdepolarizations may create a directional triggered activity to initiate reentrant ventricular tachyarrhythmias	27
Tumor spheroid elasticity estimation using mechano-microscopy combined with a conditional generative adversarial network	27
A Physics-Integrated Deep Learning Approach for Patient-Specific Non-Newtonian Blood Viscosity Assessment using PPG	27
MEMOL: Mixture of experts for multimodal learning through multi-head attention to predict drug toxicity	27
AERMNet: Attention-enhanced relational memory network for medical image report generation	27
Theoretical prediction of early afterdepolarization-evoked triggered activity formation initiating ventricular reentrant arrhythmias	27
Interpretable epidemic state estimation via rule based modeling	27
A simple EEG-based tool to guide therapeutic hypothermia decisions in neonatal hypoxic-ischemic encephalopathy	27
AutoDPS: An unsupervised diffusion model based method for multiple degradation removal in MRI	27
Precise prediction of multiple anticancer drug efficacy using multi target regression and support vector regression analysis	27
Hemolysis performance investigation of aortic valve pump based on computational fluid dynamics and entropy production theory	27
From 2D to 3D: Automated ultrasound segmentation and cross-sectional validation in murine tumor models	27
Developing a reduced order model for pulsatile blood flow simulations using minimal three-dimensional simulation data	26
Lightweight convolution transformer for cross-patient seizure detection in multi-channel EEG signals	26
Masked hypergraph learning for weakly supervised histopathology whole slide image classification	26
Real-time ultrasound shear wave elastography using a local phase gradient	26
Assessing the impact of tear direction in coronary artery dissection on thrombosis development: A hemodynamic computational study	26
Computer-aided diagnostic system for hypertensive retinopathy: A review	26
Enhancing multimodal medical image analysis with Slice-Fusion: A novel fusion approach to address modality imbalance	26
Altered dynamic joint space in the lateral condyle compartment following medial unicompartmental knee arthroplasty	26
Cross-modal alignment and contrastive learning for enhanced cancer survival prediction	26
Multi-event survival analysis through dynamic multi-modal learning for ICU mortality prediction	26
Artery fragment guided approach for enhancing cerebral aneurysm detection in TOF-MRA imaging	26
Dual-path neural network extracts tumor microenvironment information from whole slide images to predict molecular typing and prognosis of Glioma	26
Radiomics feature analysis for survival prediction in multiple myeloma: An automated PET/CT approach	25
A novel mono-physics particle-based approach for the simulation of cardiovascular fluid-structure interaction problems	25
CEP-IP: An explainable framework for cell subpopulation identification in single-cell transcriptomics	25
Attentional decoder networks for chest X-ray image recognition on high-resolution features	25
3D-MRI super-resolution reconstruction using multi-modality based on multi-resolution CNN	25
Classification of recurrent major depressive disorder using a residual denoising autoencoder framework: Insights from large-scale multisite fMRI data	25
Skin lesion segmentation using two-phase cross-domain transfer learning framework	25
MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms	25
Machine learning approach to investigate pregnancy and childbirth risk factors of sleep problems in early adolescence: Evidence from two cohort studies	25
LivXAI-Net: An explainable AI framework for liver disease diagnosis with IoT-based real-time monitoring support	25
Physics-Informed Graph Neural Networks to solve 1-D equations of blood flow	25
Inhalation exposure and particle deposition across 16 nonhuman primate airway models using computational fluid–particle dynamics for allometric extrapolation	25
Optimization of thread configuration in dental implants through regulating the mechanical stimuli in neighboring bone	25
DAX-Net: A dual-branch dual-task adaptive cross-weight feature fusion network for robust multi-class cancer classification in pathology images	25
CellViT++: Energy-efficient and adaptive cell segmentation and classification using foundation models	25
Artificial intelligence approaches for non-invasive diabetes prediction using ECG signals: A systematic review	25
PredictMed-epilepsy: A multi-agent based system for epilepsy detection and prediction in neuropediatrics	25
Interactive polar diagrams for model comparison	25
Skin lesion classification based on two-modal images using a multi-scale fully-shared fusion network	25
Automatic prostate and peri-prostatic fat segmentation based on pyramid mechanism fusion network for T2-weighted MRI	24
Quantum LBP-driven heart sound analysis with quality assessment in real-world noisy environments	24
Patient-ventilator interaction—Development of a mathematical model of the respiratory center	24
Multimodal fusion of tomographic sequences of medical images: MRE spatially enhanced by MRI	24
Gluclas: A software for computer-aided modulation of glucose infusion in glucose clamp experiments	24
Model-driven optimal experimental design for calibrating cardiac electrophysiology models	24
Swirl-inducing innovations for preventing vena cava filter blockage: Theoretical and experimental validation	24
GICAF-Net: A cross-attentional graph-image fusion network for hyperspectral pathological diagnosis of FNH and HCC	24
An explainable machine learning approach for hospital emergency department visits forecasting using continuous training and multi-model regression	24
Bioinformatic assay reveal the potential mechanism of Guizhi-Shaoyao-Zhimu decoction against rheumatoid arthritis and mild-to-moderate COVID-19	24
A novel scoring approach for the Wolf Motor Function Test in stroke survivors using motion-sensing technology and machine learning: A preliminary study	24
Dual attention mechanism network for lung cancer images super-resolution	24
Mimicking cancer therapy in an agent-based model: The case of hepatoblastoma	24
Increasing Robustness of Intracortical Brain-Computer Interfaces for Recording Condition Changes via Data Augmentation	24