Computer Methods and Programs in Biomedicine

Article	Citations
Identifying the patient harms to include in an in silico clinical trial	609
CPSS: Fusing consistency regularization and pseudo-labeling techniques for semi-supervised deep cardiovascular disease detection using all unlabeled electrocardiograms	334
Real-time soft body dissection simulation with parallelized graph-based shape matching on GPU	288
An interactive and realistic phantom for cricothyroidotomy simulation of a patient with obesity through a reusable design using 3D-printing and Arduino	238
Editorial Board	232
4-dimensional local radial basis function interpolation of large, uniformly spaced datasets	214
Dual-modeling computational framework of magnetoelectric core-shell nanoparticles and nanochain for wireless peripheral nerve regeneration	210
MSigSeg: An R package for multiple signals segmentation	167
Prediction of neoadjuvant therapy response to HER2-positive and triple-negative breast cancer: a multicenter proof-of-concept study	163
Finite element analysis of conductive hearing loss caused by fixation and detachment of ligament and tendon in the middle ear	140
VesselKnife – software for the analysis of tubular structures in biomedical images	127
Unsupervised band selection of medical hyperspectral images guided by data gravitation and weak correlation	119
Importance of the enhanced cooling system for more spherical ablation zones: Numerical simulation, ex vivo and in vivo validation	112
VOC-DL: Deep learning prediction model for COVID-19 based on VOC virus variants	108
Raw photoplethysmogram waveforms versus peak-to-peak intervals for machine learning detection of atrial fibrillation: Does waveform matter?	107
TiDE-Net: A time-guided dual-encoder ResUNet for Positron Emission Tomography (PET) image denoising	102
Using machine learning models for predicting monthly iPTH levels in hemodialysis patients	100
Prediction of the mode of delivery using artificial intelligence algorithms	99
Influence of genetic mutations to atria vulnerability to atrial fibrillation: An in-silico 3D human atria study	97
Oblique lateral interbody fusion: role of the elastic modulus of the cage material in mechanically induced osteogenesis	91
MEFA-Unet: Multi-scale feature extraction and fusion attentional unet for segmenting short process of incus in otologic microsurgical scenarios	90
Integrative analysis of RNA modification-related gene PUS7 in diagnosis, prognosis, and tumor microenvironment of hepatocellular carcinoma	89
A temporal convolutional network-based approach and a benchmark dataset for colonoscopy video temporal segmentation	88
SIMUS3: An open-source simulator for 3-D ultrasound imaging	84
Biomechanical analysis of all-polyethylene total knee arthroplasty on periprosthetic tibia using the finite element method	82

Unsupervised domain adaptation for nuclei segmentation: Adapting from hematoxylin & eosin stained slides to immunohistochemistry stained slides using a curriculum approach	81
Evaluation of deep learning training strategies for the classification of bone marrow cell images	81
A cloud-based consultation and collaboration system for radiotherapy: Remote decision support services for community radiotherapy centers	79
Modelling lower-limb peripheral arterial disease using clinically available datasets: impact of inflow boundary conditions on hemodynamic indices for restenosis prediction	78
Multimodal radiomics based on lesion connectome predicts stroke prognosis	75
Temporal convolutional neural network-based feature extraction and asynchronous channel information fusion method for heart abnormality detection in phonocardiograms	75
Differential evolution method to find optimal location of a single-element transducer for transcranial focused ultrasound therapy	75
CAPNet: Context attention pyramid network for computer-aided detection of microcalcification clusters in digital breast tomosynthesis	75
IODeep: An IOD for the introduction of deep learning in the DICOM standard	74
A Graph-guided Hybrid Regularization Method For Bioluminescence Tomography	74
MBGA-Net: A multi-branch graph adaptive network for individualized motor imagery EEG classification	73
A study on brain tumor dynamics in two-dimensional irregular domain with variable-order time-fractional derivative	71
Modelling of cardiac biventricular electromechanics with coronary blood flow to investigate the influence of coronary arterial motion on coronary haemodynamic	70
A real-time computer-aided diagnosis method for hydatidiform mole recognition using deep neural network	69
CUAMT: A MRI semi-supervised medical image segmentation framework based on contextual information and mixed uncertainty	69
The impact of small movements with dual lumen cannulae during venovenous extracorporeal membrane oxygenation: A computational fluid dynamics analysis	68
Cuffless blood pressure estimation using chaotic features of photoplethysmograms and parallel convolutional neural network	65
From local counterfactuals to global feature importance: efficient, robust, and model-agnostic explanations for brain connectivity networks	63
Detecting optimal biomarkers in ovarian cancer cells from high-dimensional mRNA expression data using machine learning	63
Optimal machine learning methods for prediction of high-flow nasal cannula outcomes using image features from electrical impedance tomography	62
An automatic pipeline for atlas-based fetal and neonatal brain segmentation and analysis	62
SC-Net: Symmetrical conical network for colorectal pathology image segmentation	60
FMCW radar based high-precision gridless non-contact vital signs monitoring for Internet of Medical Things	60
Lung nodule classification using radiomics model trained on degraded SDCT images	60
An ensemble classifier for emotion classification from EEG and GSR signals for autism detection	60
CTGAN-driven synthetic data generation: A multidisciplinary, expert-guided approach (TIMA)	59
Light&fast generative adversarial network for high-fidelity CT image synthesis of liver tumor	59
Fear of falling in community-dwelling older adults: What their gait acceleration pattern reveals	57
Computer-aided detection and segmentation of malignant melanoma lesions on whole-body 18	56
Medical image super-resolution reconstruction algorithms based on deep learning: A survey	56
A novel MCF-Net: Multi-level context fusion network for 2D medical image segmentation	56
KUB-UNet: Segmentation of Organs of Urinary System from a KUB X-ray Image	55
S-Net: A novel shallow network for enhanced detail retention in medical image segmentation	55
Health classification of Meibomian gland images using keratography 5M based on AlexNet model	54
Simulation-driven optimization of insulin therapy profiles in a commercial hybrid closed-loop system	54
A computational method to predict cerebral perfusion flow after endovascular treatment based on invasive pressure and resistance	54
A myocardial reorientation method based on feature point detection for quantitative analysis of PET myocardial perfusion imaging	54
Disease X epidemic control using a stochastic model and a deterministic approximation: Performance comparison with and without parameter uncertainties	52
Multi-scale dual-channel feature embedding decoder for biomedical image segmentation	52
Artificial intelligence model for tumoral clinical decision support systems	52
Reallocation of cutaneous and global blood circulation during sauna bathing through a closed-loop model	51
FM-Net: Deep Learning Network for the Fundamental Matrix Estimation from Biplanar Radiographs	50
Quantitative cervical spine injury responses in whiplash loading with a numerical method of natural neural reflex consideration	50
A numerical simulation study of soft tissue resection for low-damage precision cancer surgery	50
PregGAN: A prognosis prediction model for breast cancer based on conditional generative adversarial networks	49
Missing data imputation using utility-based regression and sampling approaches	49
Extension of physical activity recognition with 3D CNN using encrypted multiple sensory data to federated learning based on multi-key homomorphic encryption	49
Integrating prior knowledge with deep learning for optimized quality control in corneal images: A multicenter study	49
In-silico neuro musculoskeletal model reproduces the movement types obtained by spinal micro stimulation	49
Multi-scale simulation of red blood cell trauma in large-scale high-shear flows after Norwood operation	48

Multi-electrode catheter PFA: Computational modeling and in vivo validation of lesion dynamics under energy-dose variants	48
TransAnno-Net: A Deep Learning Framework for Accurate Cell Type Annotation of Mouse Lung Tissue Using Self-supervised Pretraining	48
Data-driven sleep structure deciphering based on cardiorespiratory signals	48
Predicting the Risk of Type B Aortic Dissection Using Hemodynamic Parameters in Aortic Arches: A Comparative Study between Healthy and Repaired Aortas	47
Editorial Board	45
PyMIC: A deep learning toolkit for annotation-efficient medical image segmentation	45
Editorial Board	45
Self-supervised learning with self-distillation on COVID-19 medical image classification	45
Retinex-qDPC: Automatic background-rectified quantitative differential phase contrast imaging	45
Effect of pulmonary regurgitation on cardiac functions based on a human bi-ventricle model	44
A probabilistic generative model to discover the treatments of coexisting diseases with missing data	44
MRCON-Net: Multiscale reweighted convolutional coding neural network for low-dose CT imaging	44
Phantom study of an in-house amplitude-gating respiratory method with silicon photomultiplier technology positron emission tomography/computed tomography	44
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	43
United multi-task learning for abdominal contrast-enhanced CT synthesis through joint deformable registration	43
Localizing the seizure onset zone and predicting the surgery outcomes in patients with drug-resistant epilepsy: A new approach based on the causal network	42
Molecular dynamics simulation of hyaluronic acid hydrogels: Effect of water content on mechanical and tribological properties	42
An improved binary particle swarm optimization algorithm for clinical cancer biomarker identification in microarray data	42
Translating medical image to radiological report: Adaptive multilevel multi-attention approach	42
CRMIPred: Identifying the spatial interactions among cis-regulatory modules via considering their cross-attended epigenetic profiles	41
A multi-task learning model with reinforcement optimization for ASD comorbidity discrimination	41
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	41
SMD-YOLO: An efficient and lightweight detection method for mask wearing status during the COVID-19 pandemic	41
A multiconsistent computational methodology to resolve a diffusive epidemiological system with effects of migration, vaccination and quarantine	41
Coronary artery disease severity and location detection using deep-mining-based magnetocardiography pattern features	41
Recurrence quantification analysis of rs-fMRI data: A method to detect subtle changes in the TgF344-AD rat model	40
Phys-DAT: A physiologically-based pharmacokinetic model for unraveling the dissolution, transit and absorption processes using PhysPK®	39
A neural network framework for immediate temperature prediction of surgical hand-held drilling	39
Improving convolutional neural network learning based on a hierarchical bezier generative model for stenosis detection in X-ray images	39
A simple agent-based hybrid model to simulate the biophysics of glioblastoma multiforme cells and the concomitant evolution of the oxygen field	39
SFTNet: A microexpression-based method for depression detection	39
Regularized multi-task learning with individual-feature-based task correlations for Alzheimer’s cognitive score prediction	39
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”	38
Performance and limitations of a supervised deep learning approach for the histopathological Oxford Classification of glomeruli with IgA nephropathy	38
Corrigendum to “Segmentation of skin layers on HFUS images using the attention mechanism”, [Computer Methods and Programs in Biomedicine, 263 (2025) 108668]	37
Predicting 6-minute walking test outcomes in patients with chronic obstructive pulmonary disease without physical performance measures	37
Multicentric intelligent cardiotocography signal interpretation using deep semi-supervised domain adaptation via minimax entropy and domain invariance	37
Dynamic elastic modulus assessment of the early degeneration model of an intervertebral disc in cynomolgus monkeys with one strike loading	37
Digital signal extraction approach for cardiotocography image	37
Haemosync: A synchronisation algorithm for multimodal haemodynamic signals	36
Automatic registration of dental CT and 3D scanned model using deep split jaw and surface curvature	36
Modified Theoretical Model Predicts Radial Support Capacity of Polymer Braided Stents	36
Corticosteroid sensitivity detection in sepsis patients using a personalized data mining approach: A clinical investigation	36
Facial expressions to identify post-stroke: A pilot study	36
A new computational pipeline for multicompartment modeling of liver perfusion	36
Evaluation of the linear and nonlinear classifiers for distinguishing between healthy subjects and patients with valvular heart diseases based on electrocardiograms, seismocardiograms, and gyrocardiog	35
Editorial Board	35
gACSON software for automated segmentation and morphology analyses of myelinated axons in 3D electron microscopy	35
Rad4XCNN: A new agnostic method for post-hoc global explanation of CNN-derived features by means of Radiomics	35
Exploring emotional climate recognition in peer conversations through bispectral features and affect dynamics	35
DARVIC: Dihedral angle-reliant variant impact classifier for functional prediction of missense VUS	35
Editorial Board	35
Editorial Board	35
ML3CNet: Non-local means-assisted automatic framework for lung cancer subtypes classification using histopathological images	35
SP-XTIN: A single projection grating-based X-ray tri-contrast imaging network	35
An accurate and trustworthy deep learning approach for bladder tumor segmentation with uncertainty estimation	35
Light scattering imaging modal expansion cytometry for label-free single-cell analysis with deep learning	35
Lesion attention guided neural network for contrast-enhanced mammography-based biomarker status prediction in breast cancer	34
Multi-target reconstruction based on subspace decision optimization for bioluminescence tomography	34
Tailored cancer therapy by magnetic nanoparticle hyperthermia: A virtual scenario simulation method	34
A novel endoscopic posterior cervical decompression and interbody fusion technique: Feasibility and biomechanical analysis	34
Parameter quantification for oxygen transport in the human brain	34
MEDUSA©: A novel Python-based software ecosystem to accelerate brain-computer interface and cognitive neuroscience research	34
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	34
Automatic segmentation and CT-based deep learning radiomics nomogram for predicting overall survival in patients with small cell lung cancer: A multicenter cohort study	34
Enlarging the thermal coagulation volume during thermochemical ablation with alternating acid-base injection by shortening the injection interval: A computational study	34
Progression of blood-borne viruses through bloodstream: A comparative mathematical study	34
Human-computer interaction on virtual reality-based training system for vascular interventional surgery	33
EESCN: A novel spiking neural network method for EEG-based emotion recognition	33
Image-based Artificial Intelligence models in the diagnosis and classification of vascular anomalies of the soft tissue in the head and neck	33
Dynamic simulation and analysis of the influence of urethral morphological changes on urodynamics after benign prostatic hyperplasia surgery: A computational fluid dynamics study	33
Neonatal EEG seizure detection using a new signal structural complexity measure based on matching pursuit decomposition with nonstationary dictionary	33
Effective active learning in digital pathology: A case study in tumor infiltrating lymphocytes	33
Considering population variability of electrophysiological models improves the in silico assessment of drug-induced torsadogenic risk	33
Sensitivity analysis of paediatric knee kinematics to the graft surgical parameters during anterior cruciate ligament reconstruction: A sequentially linked neuromusculoskeletal-finite element analysis	33
MM-CCNB: Essential protein prediction using MAX-MIN strategies and compartment of common neighboring approach	33
A novel CFD-based computed index of microcirculatory resistance (IMR) derived from coronary angiography to assess coronary microcirculation	33
Numerical study on optimization of quantitative treatment conditions for skin cancer photothermal therapy considering multiple blood vessels	33
An agent-based model to assess large-scale COVID-19 vaccination campaigns for the Italian territory: The case study of Lombardy region	33
From free‐text electronic health records to structured cohorts: Onconum, an innovative methodology for real‐world data mining in breast cancer	33

GCW-UNet segmentation of cardiac magnetic resonance images for evaluation of left atrial enlargement	33
A robust myoelectric pattern recognition framework based on individual motor unit activities against electrode array shifts	33
Robust prediction of parameterized cardiovascular hemodynamics using deep operator networks with time normalization	32
mvLognCorrEst: an R package for sampling from multivariate lognormal distributions and estimating correlations from uncomplete correlation matrix	32
NeuroDM: Decoding and visualizing human brain activity with EEG-guided diffusion model	32
Nonlinear dose-response relationship in tDCS-induced brain network synchrony: A resting-state whole-brain model analysis	32
Assessing ChatGPT's ability to emulate human reviewers in scientific research: A descriptive and qualitative approach	32
Towards robust multimodal ultrasound classification for liver tumor diagnosis: A generative approach to modality missingness	32
Gait performance in toddlers born preterm: A sensor based quantitative characterization	32
CAD-RADS scoring of coronary CT angiography with Multi-Axis Vision Transformer: A clinically-inspired deep learning pipeline	32
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
A practical strategy for data assimilation of cerebral intra-aneurysmal flows using a variational method with boundary control of velocity	31
A Multi-physics model of flow from coronary angiography: Insights to microvascular function	31
A Medical image segmentation model with auto-dynamic convolution and location attention mechanism	31
Characterization of mechanical properties of adult chests during pre-hospital manual chest compressions through a simple viscoelastic model	31
Integrating multimodal data and deep learning for functional assessment and rehabilitation prediction after cerebral hemorrhage	31
Monte Carlo modeling of hepatic steatosis based on stereology and spatial distribution of fat droplets	31
PySERA: Open-Source Standardized Python Library for Automated, Scalable, and Reproducible Handcrafted and Deep Radiomics	31
A risk and credibility framework for in silico clinical trials of medical devices	31
The role of AI for improved management of breast cancer: Enhanced diagnosis and health disparity mitigation	31
Automating COVID-19 epidemiological situation reports based on multiple data sources, the Netherlands, 2020 to 2023	30
Recent advancements and future directions in automatic swallowing analysis via videofluoroscopy: A review	30
A high-fidelity geometric multiscale hemodynamic model for predicting myocardial ischemia	30
Effect of a reduced arterial axial pre-stretch ratio during aging on the cardiac output and cerebral blood flow in the healthy elders	30
AutoDPS: An unsupervised diffusion model based method for multiple degradation removal in MRI	30
Surgical procedure prediction using medical ontological information	30
Screening chronic myeloid leukemia neutrophils using a novel 3-Dimensional Spectral Gradient Mapping algorithm on hyperspectral images	30
Experimental and computational model approach to assess the photothermal effects in transparent nanocrystalline yttria stabilized zirconia cranial implant	30
The synergy of cybernetical intelligence with medical image analysis for deep medicine: A methodological perspective	30
An end-to-end framework for intima media measurement and atherosclerotic plaque detection in the carotid artery	30
Chained occurrences of early afterdepolarizations may create a directional triggered activity to initiate reentrant ventricular tachyarrhythmias	29
BGCSL: An unsupervised framework reveals the underlying structure of large-scale whole-brain functional connectivity networks	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
Theoretical prediction of early afterdepolarization-evoked triggered activity formation initiating ventricular reentrant arrhythmias	29
Physics-Informed Graph Neural Networks to solve 1-D equations of blood flow	29
Influence of adaptive denoising on Diffusion Kurtosis Imaging at 3T and 7T	29
Classification of recurrent major depressive disorder using a residual denoising autoencoder framework: Insights from large-scale multisite fMRI data	29
BAPCP: A comprehensive and user-friendly web tool for identifying biomarkers from protein microarray technologies	29
A deep dive into the static force transmission of the human masticatory system and its biomechanical effects on the temporomandibular joint	29
AERMNet: Attention-enhanced relational memory network for medical image report generation	29
BaroWavelet: An R-based tool for dynamic baroreflex evaluation through wavelet analysis techniques	29
Altered dynamic joint space in the lateral condyle compartment following medial unicompartmental knee arthroplasty	28
Real-time estimation of lung deformation from body surface using a general CoordConv CNN	28
Interactive polar diagrams for model comparison	28
Precise prediction of multiple anticancer drug efficacy using multi target regression and support vector regression analysis	28
An expert review of the inverse problem in electrocardiographic imaging for the non-invasive identification of atrial fibrillation drivers	28
Towards open-set myoelectric gesture recognition via dual-perspective inconsistency learning	28
DE-MRI myocardial fibrosis segmentation and classification model based on multi-scale self-supervision and transformer	28
A real-time reconstructed grid method for soft tissue cutting and haptic	28
Dual center validation of deep learning for automated multi-label segmentation of thoracic anatomy in bedside chest radiographs	28
Patient-specific fluid-structure interaction modeling of cerebral aneurysm: influence of wall compliance, tissue prestress, and blood rheology	28
4D-Precise: Learning-based 3D motion estimation and high temporal resolution 4DCT reconstruction from treatment 2D+t X-ray projections	28
Noninvasive and fast method of calculation for instantaneous wave-free ratio based on haemodynamics and deep learning	28
Optimization of thread configuration in dental implants through regulating the mechanical stimuli in neighboring bone	28
High-order mesoscale modeling with geometrically conforming gray/white matter interface for traumatic brain injury	28
Endoscopic versus laparoscopic bariatric procedures: A computational biomechanical study through a patient-specific approach	28
Hemolysis performance investigation of aortic valve pump based on computational fluid dynamics and entropy production theory	27
Developing a reduced order model for pulsatile blood flow simulations using minimal three-dimensional simulation data	27
Enhancing multimodal medical image analysis with Slice-Fusion: A novel fusion approach to address modality imbalance	27
Interpretable epidemic state estimation via rule based modeling	27
Skin lesion segmentation using two-phase cross-domain transfer learning framework	27
Symbolic knowledge extraction for explainable nutritional recommenders	27
Scale resolving simulations of the effect of glottis motion and the laryngeal jet on flow dynamics during respiration	27
Radiomics feature analysis for survival prediction in multiple myeloma: An automated PET/CT approach	27
PredictMed-epilepsy: A multi-agent based system for epilepsy detection and prediction in neuropediatrics	27
Tumor spheroid elasticity estimation using mechano-microscopy combined with a conditional generative adversarial network	26
Masked hypergraph learning for weakly supervised histopathology whole slide image classification	26
MEMOL: Mixture of experts for multimodal learning through multi-head attention to predict drug toxicity	26
DAX-Net: A dual-branch dual-task adaptive cross-weight feature fusion network for robust multi-class cancer classification in pathology images	26
Multi-event survival analysis through dynamic multi-modal learning for ICU mortality prediction	26
CellViT++: Energy-efficient and adaptive cell segmentation and classification using foundation models	26
Computer-aided diagnostic system for hypertensive retinopathy: A review	26
A simple EEG-based tool to guide therapeutic hypothermia decisions in neonatal hypoxic-ischemic encephalopathy	26
Computational simulation of cellular proliferation using a meshless method	26
Real-time ultrasound shear wave elastography using a local phase gradient	26
Cross-modal alignment and contrastive learning for enhanced cancer survival prediction	26
Inhalation exposure and particle deposition across 16 nonhuman primate airway models using computational fluid–particle dynamics for allometric extrapolation	26
3D-MRI super-resolution reconstruction using multi-modality based on multi-resolution CNN	26
LivXAI-Net: An explainable AI framework for liver disease diagnosis with IoT-based real-time monitoring support	26
A Markov Chain methodology for care pathway mapping using health insurance data, a study case on pediatric TBI	26
Classification of mindfulness experiences from gamma-band effective connectivity: Application of machine-learning algorithms on resting, breathing, and body scan	25
The impact of arterial cannula direction in central venoarterial extracorporeal membrane oxygenation on aortic hemodynamic characteristics under various perfusion conditions	25
Articulating target-mining techniques to disinter Alzheimer's specific targets for drug repurposing	25
Dual-path neural network extracts tumor microenvironment information from whole slide images to predict molecular typing and prognosis of Glioma	25
Bioinformatic assay reveal the potential mechanism of Guizhi-Shaoyao-Zhimu decoction against rheumatoid arthritis and mild-to-moderate COVID-19	25
A multi-task fusion model based on a residual–Multi-layer perceptron network for mammographic breast cancer screening	25
Automatic prostate and peri-prostatic fat segmentation based on pyramid mechanism fusion network for T2-weighted MRI	25
Attentional decoder networks for chest X-ray image recognition on high-resolution features	25
Skin lesion classification based on two-modal images using a multi-scale fully-shared fusion network	25
Gluclas: A software for computer-aided modulation of glucose infusion in glucose clamp experiments	25
A deep sift convolutional neural networks for total brain volume estimation from 3D ultrasound images	25
Harnessing machine learning models for non-invasive pre-diabetes screening in children and adolescents	25
A Physics-Integrated Deep Learning Approach for Patient-Specific Non-Newtonian Blood Viscosity Assessment using PPG	25
MemBrain: A deep learning-aided pipeline for detection of membrane proteins in Cryo-electron tomograms	25