Semantic Building Blocks in Genetic Programming

In this paper we present a new mechanism for studying the impact of subtree crossover in terms of semantic building blocks. This approach allows us to completely and compactly describe the semantic action of crossover, and provide insight into what does (or doesn’t) make crossover effective. Our results make it clear that a very high proportion of crossover events (typically over 75% in our experiments) are guaranteed to perform no immediately useful search in the semantic space. Our findings also indicate a strong correlation between lack of progress and high proportions of fixed contexts. These results then suggest several new, theoretically grounded, research areas

Enumerating Building Block Semantics in Genetic Programming

This report provides a collection of definitions for the semantics of sub-trees and contexts as manipulated by standard sub-tree crossover in genetic programming (GP). These definitions allow us to completely and compactly describe the exact semantics of the components manipulated by sub-tree crossover, and the semantic results of those interactions. Sub- sequent work shows how these definitions can be used to collect valuable data about the available diversity in a GP population and the opportunities available to sub-tree crossover

Clinical observation of diminished bone quality and quantity through longitudinal HR-pQCT-derived remodeling and mechanoregulation.

High resolution peripheral quantitative computed tomography (HR-pQCT) provides methods for quantifying volumetric bone mineral density and microarchitecture necessary for early diagnosis of bone disease. When combined with a longitudinal imaging protocol and finite element analysis, HR-pQCT can be used to assess bone formation and resorption (i.e., remodeling) and the relationship between this remodeling and mechanical loading (i.e., mechanoregulation) at the tissue level. Herein, 25 patients with a contralateral distal radius fracture were imaged with HR-pQCT at baseline and 9-12 months follow-up: 16 patients were prescribed vitamin D3 with/without calcium supplement based on a blood biomarker measures of bone metabolism and dual-energy X-ray absorptiometry image-based measures of normative bone quantity which indicated diminishing (n = 9) or poor (n = 7) bone quantity and 9 were not. To evaluate the sensitivity of this imaging protocol to microstructural changes, HR-pQCT images were registered for quantification of bone remodeling and image-based micro-finite element analysis was then used to predict local bone strains and derive rules for mechanoregulation. Remodeling volume fractions were predicted by both average values of trabecular and cortical thickness and bone mineral density (R2 > 0.8), whereas mechanoregulation was affected by dominance of the arm and group classification (p < 0.05). Overall, longitudinal, extended HR-pQCT analysis enabled the identification of changes in bone quantity and quality too subtle for traditional measures

Maple scripts for the calculation of Hubbard matrices and their subsequent downfolding by Loewdin's partitioning

We provide here small Maple scripts for the calculation of Hubbard matrices and their subsequent downfolding by Loewdin's partitionin

Maple scripts for the calculation of Hubbard matrices and their subsequent downfolding by Loewdin's partitioning

We provide here small Maple scripts for the calculation of Hubbard matrices and their subsequent downfolding by Loewdin's partitionin

Validation of HR-pQCT against micro-CT for morphometric and biomechanical analyses: A review

High-resolution peripheral quantitative computed-tomography (HR-pQCT) has the potential to become a powerful clinical assessment and diagnostic tool. Given the recent improvements in image resolution, from 82 to 61 μm, this technology may be used to accurately quantify in vivo bone microarchitecture, a key biomarker of degenerative bone diseases. However, computational methods to assess bone microarchitecture were developed for micro computed tomography (micro-CT), a higher-resolution technology only available for ex vivo studies, and validation of these computational analysis techniques against the gold-standard micro-CT has been inconsistent and incomplete. Herein, we review methods for segmentation of bone compartments and microstructure, quantification of bone morphology, and estimation of mechanical strength using finite-element analysis, highlighting the need throughout for improved standardization across the field. Studies have relied on homogenous datasets for validation, which does not allow for robust comparisons between methods. Consequently, the adaptation and validation of novel segmentation approaches has been slow to non-existent, with most studies still using the manufacturer's segmentation for morphometric analysis despite the existence of better performing alternative approaches. The promising accuracy of HR-pQCT for capturing morphometric indices is overshadowed by considerable variability in outcomes between studies. For finite element analysis (FEA) methods, the use of disparate material models and FEA tools has led to a fragmented ability to assess mechanical bone strength with HR-pQCT. Further, the scarcity of studies comparing 62 μm HR-pQCT to the gold standard micro-CT leaves the validation of this imaging modality incomplete. This review revealed that without standardization, the capabilities of HR-pQCT cannot be adequately assessed. The need for a public, extendable, heterogeneous dataset of HR-pQCT and corresponding gold-standard micro-CT images, which would allow HR-pQCT users to benchmark existing and novel methods and select optimal methods depending on the scientific question and data at hand, is now evident. With more recent advancements in HR-pQCT, the community must learn from its past and provide properly validated technologies to ensure that HR-pQCT can truly provide value in patient diagnosis and care.ISSN:2352-187

Nonlinear voxel-based finite element model for strength assessment of healthy and metastatic proximal femurs

Nonlinear finite element (FE) models can accurately quantify bone strength in healthy and metastatic femurs. However, their use in clinical practice is limited since state-of-the-art implementations using tetrahedral meshes involve a lot of manual work for which specific modelling software and engineering knowledge are required. Voxel-based meshes could enable the transition since they are robust and can be highly automated. Therefore, the aim of this work was to bridge the modelling gap between the tetrahedral and voxel-based approach. Specifically, we validated a nonlinear voxel-based FE method relative to experimental data from 20 femurs with and without artificial metastases that had been mechanically loaded until failure. CT scans of the femurs were segmented and automatically converted into a voxel-based mesh with hexahedral elements. Nonlinear material properties were implemented in an open-source linear voxel-based FE solver by adding an additional loop to the routine such that the material properties could be adapted after each increment. Bone strength, quantified as the maximum force in the force-displacement curve, was evaluated. The results were compared to a previously established nonlinear tetrahedral FE approach as well as to the experimentally measured bone strength. The voxel-based FE model predicted the experimental bone strength very well both for healthy (R2 = 0.90, RMSE = 0.88 kN) and metastatic femurs (R2 = 0.93, RMSE = 0.64 kN). The model precision and accuracy were very similar to the ones obtained with the tetrahedral model (R2 = 0.90/0.93, RMSE = 0.90/0.64 kN for intact/metastatic respectively). The more intuitive voxel-based meshes thus quantified macroscale femoral strength equally well as state-of-the-art tetrahedral models. The robustness, high level of automation and time-efficiency (< 30 min) of the implemented workflow offer great potential for developing FE models to improve fracture risk prediction in clinical practice.status: Published onlin

Bone Mechanoregulation Allows Subject-Specific Load Estimation Based on Time-Lapsed Micro-CT and HR-pQCT in Vivo

Patients at high risk of fracture due to metabolic diseases frequently undergo long-term antiresorptive therapy. However, in some patients, treatment is unsuccessful in preventing fractures or causes severe adverse health outcomes. Understanding load-driven bone remodelling, i.e., mechanoregulation, is critical to understand which patients are at risk for progressive bone degeneration and may enable better patient selection or adaptive therapeutic intervention strategies. Bone microarchitecture assessment using high-resolution peripheral quantitative computed tomography (HR-pQCT) combined with computed mechanical loads has successfully been used to investigate bone mechanoregulation at the trabecular level. To obtain the required mechanical loads that induce local variances in mechanical strain and cause bone remodelling, estimation of physiological loading is essential. Current models homogenise strain patterns throughout the bone to estimate load distribution in vivo, assuming that the bone structure is in biomechanical homoeostasis. Yet, this assumption may be flawed for investigating alterations in bone mechanoregulation. By further utilising available spatiotemporal information of time-lapsed bone imaging studies, we developed a mechanoregulation-based load estimation (MR) algorithm. MR calculates organ-scale loads by scaling and superimposing a set of predefined independent unit loads to optimise measured bone formation in high-, quiescence in medium-, and resorption in low-strain regions. We benchmarked our algorithm against a previously published load history (LH) algorithm using synthetic data, micro-CT images of murine vertebrae under defined experimental in vivo loadings, and HR-pQCT images from seven patients. Our algorithm consistently outperformed LH in all three datasets. In silico-generated time evolutions of distal radius geometries (n = 5) indicated significantly higher sensitivity, specificity, and accuracy for MR than LH (p < 0.01). This increased performance led to substantially better discrimination between physiological and extra-physiological loading in mice (n = 8). Moreover, a significantly (p < 0.01) higher association between remodelling events and computed local mechanical signals was found using MR [correct classification rate (CCR) = 0.42] than LH (CCR = 0.38) to estimate human distal radius loading. Future applications of MR may enable clinicians to link subtle changes in bone strength to changes in day-to-day loading, identifying weak spots in the bone microstructure for local intervention and personalised treatment approaches.ISSN:2296-418