Search

Metrics optimized in complex machine learning tasks are often selected in an ad-hoc manner. It is unknown how they align with human expert perception. We explore the correlations between established quantitative segmentation quality metrics and qualitative evaluations by professionally trained human raters. Therefore, we conduct psychophysical experiments for two complex biomedical semantic segmentation problems. We discover that current standard metrics and loss functions correlate only moderately with the segmentation quality assessment of experts. Importantly, this effect is particularly pronounced for clinically relevant structures, such as the enhancing tumor compartment of glioma in brain magnetic resonance and grey matter in ultrasound imaging. It is often unclear how to optimize abstract metrics, such as human expert perception, in convolutional neural network (CNN) training. To cope with this challenge, we propose a novel strategy employing techniques of classical statistics to create complementary compound loss functions to better approximate human expert perception. Across all rating experiments, human experts consistently scored computer-generated segmentations better than the human-curated reference labels. Our results, therefore, strongly question many current practices in medical image segmentation and provide meaningful cues for future research., Accepted for publication at the Journal of Machine Learning for Biomedical Imaging (MELBA) https://melba-journal.org/2023:002

Deep Learning (DL) has the potential to optimize machine learning in both the scientific and clinical communities. However, greater expertise is required to develop DL algorithms, and the variability of implementations hinders their reproducibility, translation, and deployment. Here we present the community-driven Generally Nuanced Deep Learning Framework (GaNDLF), with the goal of lowering these barriers. GaNDLF makes the mechanism of DL development, training, and inference more stable, reproducible, interpretable, and scalable, without requiring an extensive technical background. GaNDLF aims to provide an end-to-end solution for all DL-related tasks in computational precision medicine. We demonstrate the ability of GaNDLF to analyze both radiology and histology images, with built-in support for k-fold cross-validation, data augmentation, multiple modalities and output classes. Our quantitative performance evaluation on numerous use cases, anatomies, and computational tasks supports GaNDLF as a robust application framework for deployment in clinical workflows.

Background The diffuse growth pattern of glioblastoma is one of the main challenges for improving patient survival. Computational tumor growth modeling has emerged as a promising tool to guide personalized therapy. Here, we performed clinical and biological validation of a novel, deep learning - based growth model, aiming to close the gap between the experimental state and clinical implementation. Methods 124 patients from The Cancer Genome Archive network and 397 patients from the UCSF Glioma MRI Dataset were assessed for correlations between clinical data, genetic pathway activation maps (generated with PARADIGM; TCGA only), and infiltration (Dw) as well as proliferation (r) parameters stemming from a Fisher-Kolmogorov growth model adjusted to the patients’ preoperative images using deep learning. Cox multivariable regression and Spearman correlation were performed to test for statistical significance. To further evaluate clinical potential, we performed the same growth modeling on preoperative MRI data from 30 patients of our institution and compared model-derived tumor volume and recurrence coverage with standard radiotherapy plans. Results The parameter ratio Dw/r (p p

Objective.De-centralized data analysis becomes an increasingly preferred option in the healthcare domain, as it alleviates the need for sharing primary patient data across collaborating institutions. This highlights the need for consistent harmonized data curation, pre-processing, and identification of regions of interest based on uniform criteria.Approach.Towards this end, this manuscript describes theFederatedTumorSegmentation (FeTS) tool, in terms of software architecture and functionality.Main results.The primary aim of the FeTS tool is to facilitate this harmonized processing and the generation of gold standard reference labels for tumor sub-compartments on brain magnetic resonance imaging, and further enable federated training of a tumor sub-compartment delineation model across numerous sites distributed across the globe, without the need to share patient data.Significance.Building upon existing open-source tools such as the Insight Toolkit and Qt, the FeTS tool is designed to enable training deep learning models targeting tumor delineation in either centralized or federated settings. The target audience of the FeTS tool is primarily the computational researcher interested in developing federated learning models, and interested in joining a global federation towards this effort. The tool is open sourced athttps://github.com/FETS-AI/Front-End.

Purpose Intrauterine claustrum and subplate neuron development have been suggested to overlap. As premature birth typically impairs subplate neuron development, neonatal claustrum might indicate a specific prematurity impact; however, claustrum identification usually relies on expert knowledge due to its intricate structure. We established automated claustrum segmentation in newborns. Methods We applied a deep learning-based algorithm for segmenting the claustrum in 558 T2-weighted neonatal brain MRI of the developing Human Connectome Project (dHCP) with transfer learning from claustrum segmentation in T1-weighted scans of adults. The model was trained and evaluated on 30 manual bilateral claustrum annotations in neonates. Results With only 20 annotated scans, the model yielded median volumetric similarity, robust Hausdorff distance and Dice score of 95.9%, 1.12 mm and 80.0%, respectively, representing an excellent agreement between the automatic and manual segmentations. In comparison with interrater reliability, the model achieved significantly superior volumetric similarity (p = 0.047) and Dice score (p Conclusion The developed fast and accurate automated segmentation has great potential in large-scale study cohorts and to facilitate MRI-based connectome research of the neonatal claustrum. The easy to use models and codes are made publicly available.

In-utero fetal MRI is emerging as an important tool in the diagnosis and analysis of the developing human brain. Automatic segmentation of the developing fetal brain is a vital step in the quantitative analysis of prenatal neurodevelopment both in the research and clinical context. However, manual segmentation of cerebral structures is time-consuming and prone to error and inter-observer variability. Therefore, we organized the Fetal Tissue Annotation (FeTA) Challenge in 2021 in order to encourage the development of automatic segmentation algorithms on an international level. The challenge utilized FeTA Dataset, an open dataset of fetal brain MRI reconstructions segmented into seven different tissues (external cerebrospinal fluid, grey matter, white matter, ventricles, cerebellum, brainstem, deep grey matter). 20 international teams participated in this challenge, submitting a total of 21 algorithms for evaluation. In this paper, we provide a detailed analysis of the results from both a technical and clinical perspective. All participants relied on deep learning methods, mainly U-Nets, with some variability present in the network architecture, optimization, and image pre- and post-processing. The majority of teams used existing medical imaging deep learning frameworks. The main differences between the submissions were the fine tuning done during training, and the specific pre- and post-processing steps performed. The challenge results showed that almost all submissions performed similarly. Four of the top five teams used ensemble learning methods. However, one team's algorithm performed significantly superior to the other submissions, and consisted of an asymmetrical U-Net network architecture. This paper provides a first of its kind benchmark for future automatic multi-tissue segmentation algorithms for the developing human brain in utero., Comment: Results from FeTA Challenge 2021, held at MICCAI; Manuscript submitted

Background Current guidelines for CT perfusion (CTP) in acute stroke suggest acquiring scans with a minimal duration of 60-70 s. But even then, CTP analysis can be affected by truncation artifacts. Conversely, shorter acquisitions are still widely used in clinical practice and may, sometimes, be sufficient to reliably estimate lesion volumes. We aim to devise an automatic method that detects scans affected by truncation artifacts. Methods Shorter scan durations are simulated from the ISLES’18 dataset by consecutively removing the last CTP time-point until reaching a 10 s duration. For each truncated series, perfusion lesion volumes are quantified and used to label the series as unreliable if the lesion volumes considerably deviate from the original untruncated ones. Afterwards, nine features from the arterial input function (AIF) and the vascular output function (VOF) are derived and used to fit machine-learning models with the goal of detecting unreliably truncated scans. Methods are compared against a baseline classifier solely based on the scan duration, which is the current clinical standard. The ROC-AUC, precision-recall AUC and the F1-score are measured in a 5-fold cross-validation setting. Results The best performing classifier obtained an ROC-AUC of 0.982, precision-recall AUC of 0.985 and F1-score of 0.938. The most important feature was the AIFcoverage, measured as the time difference between the scan duration and the AIF peak. When using the AIFcoverage to build a single feature classifier, an ROC-AUC of 0.981, precision-recall AUC of 0.984 and F1-score of 0.932 were obtained. In comparison, the baseline classifier obtained an ROC-AUC of 0.954, precision-recall AUC of 0.958 and F1-Score of 0.875. Conclusions Machine learning models fed with AIF and VOF features accurately detected unreliable stroke lesion measurements due to insufficient acquisition duration. The AIFcoverage was the most predictive feature of truncation and identified unreliable short scans almost as good as machine learning. We conclude that AIF/VOF based classifiers are more accurate than the scans’ duration for detecting truncation. These methods could be transferred to perfusion analysis software in order to increase the interpretability of CTP outputs.

Increased intracranial pressure is the source of most critical symptoms in patients with glioma, and often the main cause of death. Clinical interventions could benefit from non-invasive estimates of the pressure distribution in the patient's parenchyma provided by computational models. However, existing glioma models do not simulate the pressure distribution and they rely on a large number of model parameters, which complicates their calibration from available patient data. Here we present a novel model for glioma growth, pressure distribution and corresponding brain deformation. The distinct feature of our approach is that the pressure is directly derived from tumour dynamics and patient-specific anatomy, providing non-invasive insights into the patient's state. The model predictions allow estimation of critical conditions such as intracranial hypertension, brain midline shift or neurological and cognitive impairments. A diffuse-domain formalism is employed to allow for efficient numerical implementation of the model in the patient-specific brain anatomy. The model is tested on synthetic and clinical cases. To facilitate clinical deployment, a high-performance computing implementation of the model has been publicly released., Journal of the Royal Society Interface, 19 (188), ISSN:1742-5689, ISSN:1742-5662

In this work, we report the set-up and results of the Liver Tumor Segmentation Benchmark (LiTS), which was organized in conjunction with the IEEE International Symposium on Biomedical Imaging (ISBI) 2017 and the International Conferences on Medical Image Computing and Computer-Assisted Intervention (MICCAI) 2017 and 2018. The image dataset is diverse and contains primary and secondary tumors with varied sizes and appearances with various lesion-to-background levels (hyper-/hypo-dense), created in collaboration with seven hospitals and research institutions. Seventy-five submitted liver and liver tumor segmentation algorithms were trained on a set of 131 computed tomography (CT) volumes and were tested on 70 unseen test images acquired from different patients. We found that not a single algorithm performed best for both liver and liver tumors in the three events. The best liver segmentation algorithm achieved a Dice score of 0.963, whereas, for tumor segmentation, the best algorithms achieved Dices scores of 0.674 (ISBI 2017), 0.702 (MICCAI 2017), and 0.739 (MICCAI 2018). Retrospectively, we performed additional analysis on liver tumor detection and revealed that not all top-performing segmentation algorithms worked well for tumor detection. The best liver tumor detection method achieved a lesion-wise recall of 0.458 (ISBI 2017), 0.515 (MICCAI 2017), and 0.554 (MICCAI 2018), indicating the need for further research. LiTS remains an active benchmark and resource for research, e.g., contributing the liver-related segmentation tasks in \url{http://medicaldecathlon.com/}. In addition, both data and online evaluation are accessible via \url{www.lits-challenge.com}., Patrick Bilic, Patrick Christ, Hongwei Bran Li, and Eugene Vorontsov made equal contributions to this work. Published in Medical Image Analysis

Modeling of brain tumor dynamics has the potential to advance therapeutic planning. Current modeling approaches resort to numerical solvers that simulate the tumor progression according to a given differential equation. Using highly-efficient numerical solvers, a single forward simulation takes up to a few minutes of compute. At the same time, clinical applications of tumor modeling often imply solving an inverse problem, requiring up to tens of thousands of forward model evaluations when used for a Bayesian model personalization via sampling. This results in a total inference time prohibitively expensive for clinical translation. While recent data-driven approaches become capable of emulating physics simulation, they tend to fail in generalizing over the variability of the boundary conditions imposed by the patient-specific anatomy. In this paper, we propose a learnable surrogate for simulating tumor growth which maps the biophysical model parameters directly to simulation outputs, i.e. the local tumor cell densities, whilst respecting patient geometry. We test the neural solver in a Bayesian model personalization task for a cohort of glioma patients. Bayesian inference using the proposed surrogate yields estimates analogous to those obtained by solving the forward model with a regular numerical solver. The near real-time computation cost renders the proposed method suitable for clinical settings. The code is available at https://github.com/IvanEz/tumor-surrogate.

Healthcare data are inherently multimodal. Almost all data generated and acquired during a patient’s life can be hypothesized to contain information relevant to providing optimal personalized healthcare. Data sources such as ECGs, doctor’s notes, histopathological and radiological images all contribute to inform a physician’s treatment decision. However, most machine learning methods in healthcare focus on single-modality data. This becomes particularly apparent within the field of radiology, which, due to its information density, accessibility, and computational interpretability, constitutes a central pillar in the healthcare data landscape and traditionally has been one of the key target areas of medically-focused machine learning. Computer-assisted diagnostic systems of the future should be capable of simultaneously processing multimodal data, thereby mimicking physicians, who also consider a multitude of resources when treating patients. Before this background, this review offers a comprehensive assessment of multimodal machine learning methods that combine data from radiology and other medical disciplines. It establishes a modality-based taxonomy, discusses common architectures and design principles, evaluation approaches, challenges, and future directions. This work will enable researchers and clinicians to understand the topography of the domain, describe the state-of-the-art, and detect research gaps for future research in multimodal medical machine learning.

Spatial molecular profiling of complex tissues is essential to investigate cellular function in physiological and pathological states. However, methods for molecular analysis of large biological specimens imaged in 3D are lacking. Here, we present DISCO-MS, a technology that combines whole-organ/whole-organism clearing and imaging, deep-learning-based image analysis, robotic tissue extraction, and ultra-high-sensitivity mass spectrometry. DISCO-MS yielded proteome data indistinguishable from uncleared samples in both rodent and human tissues. We used DISCO-MS to investigate microglia activation along axonal tracts after brain injury and characterized early- and late-stage individual amyloid-beta plaques in a mouse model of Alzheimer's disease. DISCO-bot robotic sample extraction enabled us to study the regional heterogeneity of immune cells in intact mouse bodies and aortic plaques in a complete human heart. DISCO-MS enables unbiased proteome analysis of preclinical and clinical tissues after unbiased imaging of entire specimens in 3D, identifying diagnostic and therapeutic opportunities for complex diseases. VIDEO ABSTRACT.

Virtual reality environments offer great opportunities to study the performance of brain-computer interfaces (BCIs) in real-world contexts. As real-world stimuli are typically multimodal, their neuronal integration elicits complex response patterns. To investigate the effect of additional auditory cues on the processing of visual information, we used virtual reality to mimic safety-related events in an industrial environment while we concomitantly recorded electroencephalography (EEG) signals. We simulated a box traveling on a conveyor belt system where two types of stimuli – an exploding and a burning box – interrupt regular operation. The recordings from 16 subjects were divided into two subsets, a visual-only and an audio-visual experiment. In the visual-only experiment, the response patterns for both stimuli elicited a similar pattern – a visual evoked potential (VEP) followed by an event-related potential (ERP) over the occipital-parietal lobe. Moreover, we found the perceived severity of the event to be reflected in the signal amplitude. Interestingly, the additional auditory cues had a twofold effect on the previous findings: The P1 component was significantly suppressed in the case of the exploding box stimulus, whereas the N2c showed an enhancement for the burning box stimulus. This result highlights the impact of multisensory integration on the performance of realistic BCI applications. Indeed, we observed alterations in the offline classification accuracy for a detection task based on a mixed feature extraction (variance, power spectral density, and discrete wavelet transform) and a support vector machine classifier. In the case of the explosion, the accuracy slightly decreased by –1.64% p. in an audio-visual experiment compared to the visual-only. Contrarily, the classification accuracy for the burning box increased by 5.58% p. when additional auditory cues were present. Hence, we conclude, that especially in challenging detection tasks, it is favorable to consider the potential of multisensory integration when BCIs are supposed to operate under (multimodal) real-world conditions.

The Cerebral Aneurysm Detection and Analysis (CADA) challenge was organized to support the development and benchmarking of algorithms for detecting, analyzing, and risk assessment of cerebral aneurysms in X-ray rotational angiography (3DRA) images. 109 anonymized 3DRA datasets were provided for training, and 22 additional datasets were used to test the algorithmic solutions. Cerebral aneurysm detection was assessed using the F2 score based on recall and precision, and the fit of the delivered bounding box was assessed using the distance to the aneurysm. The segmentation quality was measured using the Jaccard index and a combination of different surface distance measures. Systematic errors were analyzed using volume correlation and bias. Rupture risk assessment was evaluated using the F2 score. 158 participants from 22 countries registered for the CADA challenge. The U-Net-based detection solutions presented by the community show similar accuracy compared to experts (F2 score 0.92), with a small number of missed aneurysms with diameters smaller than 3.5 mm. In addition, the delineation of these structures, based on U-Net variations, is excellent, with a Jaccard score of 0.92. The rupture risk estimation methods achieved an F2 score of 0.71. The performance of the detection and segmentation solutions is equivalent to that of human experts. The best results are obtained in rupture risk estimation by combining different image-based, morphological, and computational fluid dynamic parameters using machine learning methods. Furthermore, we evaluated the best methods pipeline, from detecting and delineating the vessel dilations to estimating the risk of rupture. The chain of these methods achieves an F2-score of 0.70, which is comparable to applying the risk prediction to the ground-truth delineation (0.71).

To determine the accuracy of an artificial neural network (ANN) for fully automated detection of the presence and phase of iodinated contrast agent in routine abdominal multidetector computed tomography (MDCT) scans and evaluate the effect of contrast correction for osteoporosis screening.This HIPPA-compliant study retrospectively included 579 MDCT scans in 193 patients (62.4 ± 14.6 years, 48 women). Three different ANN models (2D DenseNet with random slice selection, 2D DenseNet with anatomy-guided slice selection, 3D DenseNet) were trained in 462 MDCT scans of 154 patients (threefold cross-validation), who underwent triphasic CT. All ANN models were tested in 117 unseen triphasic scans of 39 patients, as well as in a public MDCT dataset containing 311 patients. In the triphasic test scans, trabecular volumetric bone mineral density (BMD) was calculated using a fully automated pipeline. Root-mean-square errors (RMSE) of BMD measurements with and without correction for contrast application were calculated in comparison to nonenhanced (NE) scans.The 2D DenseNet with anatomy-guided slice selection outperformed the competing models and achieved an F1 score of 0.98 and an accuracy of 98.3% in the test set (public dataset: F1 score 0.93; accuracy 94.2%). Application of contrast agent resulted in significant BMD biases (all p .001; portal-venous (PV): RMSE 18.7 mg/ml, mean difference 17.5 mg/ml; arterial (AR): RMSE 6.92 mg/ml, mean difference 5.68 mg/ml). After the fully automated correction, this bias was no longer significant (p .05; PV: RMSE 9.45 mg/ml, mean difference 1.28 mg/ml; AR: RMSE 3.98 mg/ml, mean difference 0.94 mg/ml).Automatic detection of the contrast phase in multicenter CT data was achieved with high accuracy, minimizing the contrast-induced error in BMD measurements.• A 2D DenseNet with anatomy-guided slice selection achieved an F1 score of 0.98 and an accuracy of 98.3% in the test set. In a public dataset, an F1 score of 0.93 and an accuracy of 94.2% were obtained. • Automated adjustment for contrast injection improved the accuracy of lumbar bone mineral density measurements (RMSE 18.7 mg/ml vs. 9.45 mg/ml respectively, in the portal-venous phase). • An artificial neural network can reliably reveal the presence and phase of iodinated contrast agent in multidetector CT scans ( https://github.com/ferchonavarro/anatomy_guided_contrast_c ). This allows minimizing the contrast-induced error in opportunistic bone mineral density measurements.

Purpose To develop a weakly supervised deep learning (WSDL) method that could utilize incomplete/missing survival data to predict the prognosis of extranodal natural killer/T cell lymphoma, nasal type (ENKTL) based on pretreatment 18F-FDG PET/CT results. Methods One hundred and sixty-seven patients with ENKTL who underwent pretreatment 18F-FDG PET/CT were retrospectively collected. Eighty-four patients were followed up for at least 2 years (training set = 64, test set = 20). A WSDL method was developed to enable the integration of the remaining 83 patients with incomplete/missing follow-up information in the training set. To test generalization, these data were derived from three types of scanners. Prediction similarity index (PSI) was derived from deep learning features of images. Its discriminative ability was calculated and compared with that of a conventional deep learning (CDL) method. Univariate and multivariate analyses helped explore the significance of PSI and clinical features. Results PSI achieved area under the curve scores of 0.9858 and 0.9946 (training set) and 0.8750 and 0.7344 (test set) in the prediction of progression-free survival (PFS) with the WSDL and CDL methods, respectively. PSI threshold of 1.0 could significantly differentiate the prognosis. In the test set, WSDL and CDL achieved prediction sensitivity, specificity, and accuracy of 87.50% and 62.50%, 83.33% and 83.33%, and 85.00% and 75.00%, respectively. Multivariate analysis confirmed PSI to be an independent significant predictor of PFS in both the methods. Conclusion The WSDL-based framework was more effective for extracting 18F-FDG PET/CT features and predicting the prognosis of ENKTL than the CDL method. Supplementary Information The online version contains supplementary material available at 10.1007/s00259-021-05232-3.

This study proposes an automated prostate cancer (PC) lesion characterization method based on the deep neural network to determine tumor burden onWe collectedAmong all the labeled lesions, the network achieved 99% precision, 99% recall, and an F1 score of 99% on bone lesion detection and 94%, precision 89% recall, and an F1 score of 92% on lymph node lesion detection. The segmentation accuracy is lower than the detection. The performance of the network was correlated with the amount of training data.We developed a deep neural network to characterize automatically the PC lesions on

Semantic segmentation of medical images aims to associate a pixel with a label in a medical image without human initialization. The success of semantic segmentation algorithms is contingent on the availability of high-quality imaging data with corresponding labels provided by experts. We sought to create a large collection of annotated medical image datasets of various clinically relevant anatomies available under open source license to facilitate the development of semantic segmentation algorithms. Such a resource would allow: 1) objective assessment of general-purpose segmentation methods through comprehensive benchmarking and 2) open and free access to medical image data for any researcher interested in the problem domain. Through a multi-institutional effort, we generated a large, curated dataset representative of several highly variable segmentation tasks that was used in a crowd-sourced challenge - the Medical Segmentation Decathlon held during the 2018 Medical Image Computing and Computer Aided Interventions Conference in Granada, Spain. Here, we describe these ten labeled image datasets so that these data may be effectively reused by the research community.

Our aim was to introduce and validate qPSMA, a semiautomatic software package for whole-body tumor burden assessment in prostate cancer patients using (68)Ga-prostate-specific membrane antigen (PSMA) 11 PET/CT. Methods: qPSMA reads hybrid PET/CT images in DICOM format. Its pipeline was written using Python and C++ languages. A bone mask based on CT and a normal-uptake mask including organs with physiologic (68)Ga-PSMA11 uptake are automatically computed. An SUV threshold of 3 and a liver-based threshold are used to segment bone and soft-tissue lesions, respectively. Manual corrections can be applied using different tools. Multiple output parameters are computed, that is, PSMA ligand–positive tumor volume (PSMA-TV), PSMA ligand–positive total lesion (PSMA-TL), PSMA SUV(mean), and PSMA SUV(max). Twenty (68)Ga-PSMA11 PET/CT data sets were used to validate and evaluate the performance characteristics of qPSMA. Four analyses were performed: validation of the semiautomatic algorithm for liver background activity determination, assessment of intra- and interobserver variability, validation of data from qPSMA by comparison with Syngo.via, and assessment of computational time and comparison of PSMA PET–derived parameters with serum prostate-specific antigen. Results: Automatic liver background calculation resulted in a mean relative difference of 0.74% (intraclass correlation coefficient [ICC], 0.996; 95%CI, 0.989;0.998) compared with METAVOL. Intra- and interobserver variability analyses showed high agreement (all ICCs > 0.990). Quantitative output parameters were compared for 68 lesions. Paired t testing showed no significant differences between the values obtained with the 2 software packages. The ICC estimates obtained for PSMA-TV, PSMA-TL, SUV(mean), and SUV(max) were 1.000 (95%CI, 1.000;1.000), 1.000 (95%CI, 1.000;1.000), 0.995 (95%CI, 0.992;0.997), and 0.999 (95%CI, 0.999;1.000), respectively. The first and second reads for intraobserver variability resulted in mean computational times of 13.63 min (range, 8.22–25.45 min) and 9.27 min (range, 8.10–12.15 min), respectively (P = 0.001). Highly significant correlations were found between serum prostate-specific antigen value and both PSMA-TV (r = 0.72, P < 0.001) and PSMA-TL (r = 0.66, P = 0.002). Conclusion: Semiautomatic analyses of whole-body tumor burden in (68)Ga-PSMA11 PET/CT is feasible. qPSMA is a robust software package that can help physicians quantify tumor load in heavily metastasized prostate cancer patients.

We propose the S-leaping algorithm for the acceleration of Gillespie's stochastic simulation algorithm that combines the advantages of the two main accelerated methods; the [Formula: see text]-leaping and R-leaping algorithms. These algorithms are known to be efficient under different conditions; the [Formula: see text]-leaping is efficient for non-stiff systems or systems with partial equilibrium, while the R-leaping performs better in stiff system thanks to an efficient sampling procedure. However, even a small change in a system's set up can critically affect the nature of the simulated system and thus reduce the efficiency of an accelerated algorithm. The proposed algorithm combines the efficient time step selection from the [Formula: see text]-leaping with the effective sampling procedure from the R-leaping algorithm. The S-leaping is shown to maintain its efficiency under different conditions and in the case of large and stiff systems or systems with fast dynamics, the S-leaping outperforms both methods. We demonstrate the performance and the accuracy of the S-leaping in comparison with the [Formula: see text]-leaping and R-leaping on a number of benchmark systems involving biological reaction networks.

Wall shear stress (WSS) presents an important parameter for assessing blood flow characteristics and evaluating flow-mediated lesions in the aorta.To investigate the robustness of WSS and oscillatory shear index (OSI) estimation based on 4D flow MRI against vessel wall motion, spatiotemporal resolution, and velocity encoding (VENC).Simulated and prospective.Synthetic 4D flow MRI data of the aorta, simulated using the Lattice-Boltzmann method; in vivo 4D flow MRI data of the aorta from healthy volunteers (n = 11) and patients with congenital heart defects (n = 17).1.5T; 4D flow MRI with PEAK-GRAPPA acceleration and prospective electrocardiogram triggering.Predicated upon 3D cubic B-splines interpolation of the image velocity field, WSS was estimated in mid-systole, early-diastole, and late-diastole and OSI was derived. We assessed the impact of spatiotemporal resolution and phase noise, and compared results based on tracked-using deformable registration-and static vessel wall location.Bland-Altman analysis to assess WSS/OSI differences; Hausdorff distance (HD) to assess wall motion; and Pearson's correlation coefficient (PCC) to assess correlation of HD with WSS.Synthetic data results show systematic over-/underestimation of WSS when different spatial resolution (mean ± 1.96 SD up to -0.24 ± 0.40 N/mIn addition to sufficient spatial resolution and velocity to noise ratio, accurate tracking of the vessel wall is essential for reliable image-based WSS estimation and should not be neglected if wall motion is present.2 Technical Efficacy: Stage 2 J. Magn. Reson. Imaging 2018.

Malignant growth usually leads to the depletion of oxygen (O

Differences in scanning parameters or modalities can complicate image analysis based on supervised classification. This paper presents two representation learning approaches, based on autoencoders, that address this problem by learning representations that are similar across domains. Both approaches use, next to the data representation objective, a similarity objective to minimise the difference between representations of corresponding patches from each domain. We evaluated the methods in transfer learning experiments on multi-modal brain MRI data and on synthetic data. After transforming training and test data from different modalities to the common representations learned by our methods, we trained classifiers for each of pair of modalities. We found that adding the similarity term to the standard objective can produce representations that are more similar and can give a higher accuracy in these cross-modality classification experiments.