scholarly journals Predictive Behavior of a Computational Foot/Ankle Model through Artificial Neural Networks

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Ruchi D. Chande ◽  
Rosalyn Hobson Hargraves ◽  
Norma Ortiz-Robinson ◽  
Jennifer S. Wayne
Keyword(s):  
Neural Networks ◽  
Computational Models ◽  
Predictive Performance ◽  
Imaging Data ◽  
Predictive Capability ◽  
Tissue Properties ◽  
Bony Anatomy ◽  
Ligament Stiffness ◽  
Predictive Behavior ◽  
Human Joints

Computational models are useful tools to study the biomechanics of human joints. Their predictive performance is heavily dependent on bony anatomy and soft tissue properties. Imaging data provides anatomical requirements while approximate tissue properties are implemented from literature data, when available. We sought to improve the predictive capability of a computational foot/ankle model by optimizing its ligament stiffness inputs using feedforward and radial basis function neural networks. While the former demonstrated better performance than the latter per mean square error, both networks provided reasonable stiffness predictions for implementation into the computational model.

Predictive performance modeling of Habesha brewery wastewater treatment plant using artificial neural networks

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Neural Networks ◽  
Water Quality ◽  
Wastewater Treatment ◽  
Artificial Neural Networks ◽  
Performance Modeling ◽  
Predictive Performance ◽  
Mathematical Tool ◽  
Effluent Water ◽  
Artificial Neural

Recently, process control in wastewater treatment plants (WWTPs) is, mostly accomplished through examining the quality of the water effluent and adjusting the processes through the operator’s experience. This practice is inefficient, costly and slow in control response. A better control of WTPs can be achieved by developing a robust mathematical tool for performance prediction. Due to their high accuracy and quite promising application in the field of engineering, Artificial Neural Networks (ANNs) are attracting attention in the domain of WWTP predictive performance modeling. This work focuses on applying ANN with a feed-forward, back propagation learning paradigm to predict the effluent water quality of the Habesha brewery WTP. Data of influent and effluent water quality covering approximately an 11-month period (May 2016 to March 2017) were used to develop, calibrate and validate the models. The study proves that ANN can predict the effluent water quality parameters with a correlation coefficient (R) between the observed and predicted output values reaching up to 0.969. Model architecture of 3-21-3 for pH and TN, and 1-76-1 for COD were selected as optimum topologies for predicting the Habesha Brewery WTP performance. The linear correlation between predicted and target outputs for the optimal model architectures described above were 0.9201 and 0.9692, respectively.

Machine Learning-Based Scoring Functions. Development and Applications with SAnDReS.

2020 ◽  
Vol 27 ◽  
Author(s):  
Gabriela Bitencourt-Ferreira ◽  
Camila Rizzotto ◽  
Walter Filgueira de Azevedo Junior
Keyword(s):  
Machine Learning ◽  
Binding Affinity ◽  
Drug Targets ◽  
Computational Models ◽  
Factor Xa ◽  
Coagulation Factor ◽  
Predictive Performance ◽  
Machine Learning Techniques ◽  
Scoring Functions ◽  
Molegro Virtual Docker

Background: Analysis of atomic coordinates of protein-ligand complexes can provide three-dimensional data to generate computational models to evaluate binding affinity and thermodynamic state functions. Application of machine learning techniques can create models to assess protein-ligand potential energy and binding affinity. These methods show superior predictive performance when compared with classical scoring functions available in docking programs. Objective: Our purpose here is to review the development and application of the program SAnDReS. We describe the creation of machine learning models to assess the binding affinity of protein-ligand complexes. Method: SAnDReS implements machine learning methods available in the scikit-learn library. This program is available for download at https://github.com/azevedolab/sandres. SAnDReS uses crystallographic structures, binding, and thermodynamic data to create targeted scoring functions. Results: Recent applications of the program SAnDReS to drug targets such as Coagulation factor Xa, cyclin-dependent kinases, and HIV-1 protease were able to create targeted scoring functions to predict inhibition of these proteins. These targeted models outperform classical scoring functions. Conclusion: Here, we reviewed the development of machine learning scoring functions to predict binding affinity through the application of the program SAnDReS. Our studies show the superior predictive performance of the SAnDReS-developed models when compared with classical scoring functions available in the programs such as AutoDock4, Molegro Virtual Docker, and AutoDock Vina.

scholarly journals Comparison of pretherapeutic osseous tumor volume and standard hematology for prediction of hematotoxicity after PSMA-targeted radioligand therapy

2021 ◽  
Author(s):  
Liam Widjaja ◽  
Rudolf A. Werner ◽  
Tobias L. Ross ◽  
Frank M. Bengel ◽  
Thorsten Derlin
Keyword(s):  
Multivariate Analysis ◽  
Tumor Volume ◽  
Predictive Performance ◽  
Castration Resistant Prostate Cancer ◽  
Operating Characteristics ◽  
Predictive Capability ◽  
Radioligand Therapy ◽  
Castration Resistant ◽  
Pet Ct ◽  
Late Stages

Abstract Purpose Hematotoxicity is a potentially dose-limiting adverse event in patients with metastasized castration-resistant prostate cancer (mCRPC) undergoing prostate-specific membrane antigen (PSMA)-directed radioligand therapy (RLT). We aimed to identify clinical or PSMA-targeted imaging-derived parameters to predict hematological adverse events at early and late stages in the treatment course. Methods In 67 patients with mCRPC scheduled for 177Lu-PSMA-617 RLT, pretherapeutic osseous tumor volume (TV) from 68Ga-PSMA-11 PET/CT and laboratory values were assessed. We then tested the predictive capability of these parameters for early and late hematotoxicity (according to CTCAE vers. 5.0) after one cycle of RLT and in a subgroup of 32/67 (47.8%) patients after four cycles of RLT. Results After one cycle, 10/67 (14.9%) patients developed leukocytopenia (lymphocytopenia, 39/67 [58.2%]; thrombocytopenia, 17/67 [25.4%]). A cut-off of 5.6 × 103/mm3 for baseline leukocytes was defined by receiver operating characteristics (ROC) and separated between patients with and without leukocytopenia (P < 0.001). Baseline leukocyte count emerged as a stronger predictive factor in multivariate analysis (hazard ratio [HR], 33.94, P = 0.001) relative to osseous TV (HR, 14.24, P = 0.01). After four cycles, 4/32 (12.5%) developed leukocytopenia and the pretherapeutic leukocyte cut-off (HR, 9.97, P = 0.082) tended to predict leukocytopenia better than TV (HR, 8.37, P = 0.109). In addition, a cut-off of 1.33 × 103/mm3 for baseline lymphocytes separated between patients with and without lymphocytopenia (P < 0.001), which was corroborated in multivariate analysis (HR, 21.39, P < 0.001 vs. TV, HR, 4.57, P = 0.03). After four cycles, 19/32 (59.4%) developed lymphocytopenia and the pretherapeutic cut-off for lymphocytes (HR, 46.76, P = 0.007) also demonstrated superior predictive performance for late lymphocytopenia (TV, HR, 5.15, P = 0.167). Moreover, a cut-off of 206 × 103/mm3 for baseline platelets separated between patients with and without thrombocytopenia (P < 0.001) and also demonstrated superior predictive capability in multivariate analysis (HR, 115.02, P < 0.001 vs.TV, HR, 12.75, P = 0.025). After four cycles, 9/32 (28.1%) developed thrombocytopenia and the pretherapeutic cut-off for platelets (HR, 5.44, P = 0.048) was also superior for the occurrence of late thrombocytopenia (TV, HR, 1.44, P = 0.7). Conclusions Pretherapeutic leukocyte, lymphocyte, and platelet levels themselves are strong predictors for early and late hematotoxicity under PSMA-directed RLT, and are better suited than PET-based osseous TV for this purpose.

scholarly journals Differences in subcortico-cortical interactions identified from connectome and microcircuit models in autism

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Bo-yong Park ◽  
Seok-Jun Hong ◽  
Sofie L. Valk ◽  
Casey Paquola ◽  
Oualid Benkarim ◽  
...  
Keyword(s):  
Data Exchange ◽  
Computational Models ◽  
Simulation Models ◽  
Autism Diagnostic Observation Schedule ◽  
Supervised Machine Learning ◽  
Global Network ◽  
Imaging Data ◽  
Phenotypic Data ◽  
Severity Scores ◽  
High Level

AbstractThe pathophysiology of autism has been suggested to involve a combination of both macroscale connectome miswiring and microcircuit anomalies. Here, we combine connectome-wide manifold learning with biophysical simulation models to understand associations between global network perturbations and microcircuit dysfunctions in autism. We studied neuroimaging and phenotypic data in 47 individuals with autism and 37 typically developing controls obtained from the Autism Brain Imaging Data Exchange initiative. Our analysis establishes significant differences in structural connectome organization in individuals with autism relative to controls, with strong between-group effects in low-level somatosensory regions and moderate effects in high-level association cortices. Computational models reveal that the degree of macroscale anomalies is related to atypical increases of recurrent excitation/inhibition, as well as subcortical inputs into cortical microcircuits, especially in sensory and motor areas. Transcriptomic association analysis based on postmortem datasets identifies genes expressed in cortical and thalamic areas from childhood to young adulthood. Finally, supervised machine learning finds that the macroscale perturbations are associated with symptom severity scores on the Autism Diagnostic Observation Schedule. Together, our analyses suggest that atypical subcortico-cortical interactions are associated with both microcircuit and macroscale connectome differences in autism.

scholarly journals A Neural Network Decomposition Algorithm for Mapping on Crossbar-Based Computing Systems

Electronics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 1526 ◽  
Author(s):  
Choongmin Kim ◽  
Jacob A. Abraham ◽  
Woochul Kang ◽  
Jaeyong Chung
Keyword(s):  
Neural Network ◽  
Neural Networks ◽  
Predictive Performance ◽  
Fixed Number ◽  
Decomposition Algorithm ◽  
Computing Systems ◽  
Network Decomposition ◽  
Von Neumann ◽  
Analog Computing ◽  
The Neural Network

Crossbar-based neuromorphic computing to accelerate neural networks is a popular alternative to conventional von Neumann computing systems. It is also referred as processing-in-memory and in-situ analog computing. The crossbars have a fixed number of synapses per neuron and it is necessary to decompose neurons to map networks onto the crossbars. This paper proposes the k-spare decomposition algorithm that can trade off the predictive performance against the neuron usage during the mapping. The proposed algorithm performs a two-level hierarchical decomposition. In the first global decomposition, it decomposes the neural network such that each crossbar has k spare neurons. These neurons are used to improve the accuracy of the partially mapped network in the subsequent local decomposition. Our experimental results using modern convolutional neural networks show that the proposed method can improve the accuracy substantially within about 10% extra neurons.

An efficient approach to converting three-dimensional image data into highly accurate computational models

2008 ◽  
Vol 366 (1878) ◽  
pp. 3155-3173 ◽  
Author(s):  
P.G Young ◽  
T.B.H Beresford-West ◽  
S.R.L Coward ◽  
B Notarberardino ◽  
B Walker ◽  
...  
Keyword(s):  
Mesh Generation ◽  
Computational Models ◽  
Three Dimensional ◽  
Image Data ◽  
Model Material ◽  
Imaging Data ◽  
Material Inhomogeneity ◽  
Dimensional Image ◽  
Wide Range ◽  
Impact Modelling

Image-based meshing is opening up exciting new possibilities for the application of computational continuum mechanics methods (finite-element and computational fluid dynamics) to a wide range of biomechanical and biomedical problems that were previously intractable owing to the difficulty in obtaining suitably realistic models. Innovative surface and volume mesh generation techniques have recently been developed, which convert three-dimensional imaging data, as obtained from magnetic resonance imaging, computed tomography, micro-CT and ultrasound, for example, directly into meshes suitable for use in physics-based simulations. These techniques have several key advantages, including the ability to robustly generate meshes for topologies of arbitrary complexity (such as bioscaffolds or composite micro-architectures) and with any number of constituent materials (multi-part modelling), providing meshes in which the geometric accuracy of mesh domains is only dependent on the image accuracy (image-based accuracy) and the ability for certain problems to model material inhomogeneity by assigning the properties based on image signal strength. Commonly used mesh generation techniques will be compared with the proposed enhanced volumetric marching cubes (EVoMaCs) approach and some issues specific to simulations based on three-dimensional image data will be discussed. A number of case studies will be presented to illustrate how these techniques can be used effectively across a wide range of problems from characterization of micro-scaffolds through to head impact modelling.

scholarly journals External validation of the predictive performance of population pharmacokinetic models for phenobarbital in pediatric patients

2020 ◽  
Author(s):  
Sunae Ryu ◽  
Woo Jin Jung ◽  
Zheng Jiao ◽  
Jung Woo Chae ◽  
Hwi-yeol Yun
Keyword(s):  
External Validation ◽  
Predictive Performance ◽  
Validation Dataset ◽  
Therapeutic Drug ◽  
Population Pharmacokinetic ◽  
Pharmacokinetic Models ◽  
Bayesian Forecasting ◽  
Predictive Capability ◽  
Young Infants ◽  
Simulation Based

Aim: Several studies have reported population pharmacokinetic models for phenobarbital (PB), but the predictive performance of these models has not been well documented. This study aims to do external validation of the predictive performance in published pharmacokinetic models. Methods: Therapeutic drug monitoring data collected in neonates and young infants treated with PB for seizure control, was used for external validation. A literature review was conducted through PubMed to identify population pharmacokinetic models. Prediction- and simulation-based diagnostics, and Bayesian forecasting were performed for external validation. The incorporation of size or maturity functions into the published models was also tested for prediction improvement. Results: A total of 79 serum concentrations from 28 subjects were included in the external validation dataset. Seven population pharmacokinetic studies of PB were selected for evaluation. The model by Voller et al. [27] showed the best performance concerning prediction-based evaluation. In simulation-based analyses, the normalized prediction distribution error of two models (those of Shellhaas et al. [24] and Marsot et al. [25]) obeyed a normal distribution. Bayesian forecasting with more than one observation improved predictive capability. Incorporation of both allometric size scaling and maturation function generally enhanced the predictive performance, but with marked improvement for the adult pharmacokinetic model. Conclusion: The predictive performance of published pharmacokinetic models of PB was diverse, and validation may be necessary to extrapolate to different clinical settings. Our findings suggest that Bayesian forecasting improves the predictive capability of individual concentrations for pediatrics.

scholarly journals Model-based fMRI reveals dissimilarity processes underlying base rate neglect

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Sean R O'Bryan ◽  
Darrell A Worthy ◽  
Evan J Livesey ◽  
Tyler Davis
Keyword(s):  
Computational Models ◽  
Human Subjects ◽  
Base Rate ◽  
Imaging Data ◽  
Multivoxel Pattern Analysis ◽  
Activation Patterns ◽  
Model Based ◽  
Base Rate Neglect ◽  
Rate Information ◽  
Rare Category

Extensive evidence suggests that people use base rate information inconsistently in decision making. A classic example is the inverse base rate effect (IBRE), whereby participants classify ambiguous stimuli sharing features of both common and rare categories as members of the rare category. Computational models of the IBRE have either posited that it arises from associative similarity-based mechanisms or dissimilarity-based processes that may depend upon higher-level inference. Here we develop a hybrid model, which posits that similarity- and dissimilarity-based evidence both contribute to the IBRE, and test it using functional magnetic resonance imaging data collected from human subjects completing an IBRE task. Consistent with our model, multivoxel pattern analysis reveals that activation patterns on ambiguous test trials contain information consistent with dissimilarity-based processing. Further, trial-by-trial activation in left rostrolateral prefrontal cortex tracks model-based predictions for dissimilarity-based processing, consistent with theories positing a role for higher-level symbolic processing in the IBRE.

scholarly journals Quantifying accuracy and heterogeneity in single-molecule super-resolution microscopy

2019 ◽  
Author(s):  
Hesam Mazidi ◽  
Tianben Ding ◽  
Arye Nehorai ◽  
Matthew D. Lew
Keyword(s):  
Single Molecule ◽  
Computational Models ◽  
Amyloid Fibrils ◽  
Imaging System ◽  
Simulated Data ◽  
Super Resolution ◽  
Ground Truth ◽  
Localization Algorithm ◽  
Reconstruction Algorithms ◽  
Imaging Data

The resolution and accuracy of single-molecule localization micro-scopes (SMLMs) are routinely benchmarked using simulated data, calibration “rulers,” or comparisons to secondary imaging modalities. However, these methods cannot quantify the nanoscale accuracy of an arbitrary SMLM dataset. Here, we show that by computing localization stability under a well-chosen perturbation with accurate knowledge of the imaging system, we can robustly measure the confidence of individual localizations without ground-truth knowledge of the sample. We demonstrate that our method, termed Wasserstein-induced flux (WIF), measures the accuracy of various reconstruction algorithms directly on experimental 2D and 3D data of microtubules and amyloid fibrils. We further show that WIF confidences can be used to evaluate the mismatch between computational models and imaging data, enhance the accuracy and resolution of recon-structed structures, and discover hidden molecular heterogeneities. As a computational methodology, WIF is broadly applicable to any SMLM dataset, imaging system, and localization algorithm.

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