11,666 research outputs found
Similarity-based virtual screening using 2D fingerprints
This paper summarises recent work at the University of Sheffield on virtual screening methods that use 2D fingerprint measures of structural similarity. A detailed comparison of a large number of similarity coefficients demonstrates that the well-known Tanimoto coefficient remains the method of choice for the computation of fingerprint-based similarity, despite possessing some inherent biases related to the sizes of the molecules that are being sought. Group fusion involves combining the results of similarity searches based on multiple reference structures and a single similarity measure. We demonstrate the effectiveness of this approach to screening, and also describe an approximate form of group fusion, turbo similarity searching, that can be used when just a single reference structure is available
Toward adaptive radiotherapy for head and neck patients: Uncertainties in dose warping due to the choice of deformable registration algorithm.
The aims of this work were to evaluate the performance of several deformable image registration (DIR) algorithms implemented in our in-house software (NiftyReg) and the uncertainties inherent to using different algorithms for dose warping
A GPU-based multi-criteria optimization algorithm for HDR brachytherapy
Currently in HDR brachytherapy planning, a manual fine-tuning of an objective
function is necessary to obtain case-specific valid plans. This study intends
to facilitate this process by proposing a patient-specific inverse planning
algorithm for HDR prostate brachytherapy: GPU-based multi-criteria optimization
(gMCO).
Two GPU-based optimization engines including simulated annealing (gSA) and a
quasi-Newton optimizer (gL-BFGS) were implemented to compute multiple plans in
parallel. After evaluating the equivalence and the computation performance of
these two optimization engines, one preferred optimization engine was selected
for the gMCO algorithm. Five hundred sixty-two previously treated prostate HDR
cases were divided into validation set (100) and test set (462). In the
validation set, the number of Pareto optimal plans to achieve the best plan
quality was determined for the gMCO algorithm. In the test set, gMCO plans were
compared with the physician-approved clinical plans.
Over 462 cases, the number of clinically valid plans was 428 (92.6%) for
clinical plans and 461 (99.8%) for gMCO plans. The number of valid plans with
target V100 coverage greater than 95% was 288 (62.3%) for clinical plans and
414 (89.6%) for gMCO plans. The mean planning time was 9.4 s for the gMCO
algorithm to generate 1000 Pareto optimal plans.
In conclusion, gL-BFGS is able to compute thousands of SA equivalent
treatment plans within a short time frame. Powered by gL-BFGS, an ultra-fast
and robust multi-criteria optimization algorithm was implemented for HDR
prostate brachytherapy. A large-scale comparison against physician approved
clinical plans showed that treatment plan quality could be improved and
planning time could be significantly reduced with the proposed gMCO algorithm.Comment: 18 pages, 7 figure
Simultaneous use of Individual and Joint Regularization Terms in Compressive Sensing: Joint Reconstruction of Multi-Channel Multi-Contrast MRI Acquisitions
Purpose: A time-efficient strategy to acquire high-quality multi-contrast
images is to reconstruct undersampled data with joint regularization terms that
leverage common information across contrasts. However, these terms can cause
leakage of uncommon features among contrasts, compromising diagnostic utility.
The goal of this study is to develop a compressive sensing method for
multi-channel multi-contrast magnetic resonance imaging (MRI) that optimally
utilizes shared information while preventing feature leakage.
Theory: Joint regularization terms group sparsity and colour total variation
are used to exploit common features across images while individual sparsity and
total variation are also used to prevent leakage of distinct features across
contrasts. The multi-channel multi-contrast reconstruction problem is solved
via a fast algorithm based on Alternating Direction Method of Multipliers.
Methods: The proposed method is compared against using only individual and
only joint regularization terms in reconstruction. Comparisons were performed
on single-channel simulated and multi-channel in-vivo datasets in terms of
reconstruction quality and neuroradiologist reader scores.
Results: The proposed method demonstrates rapid convergence and improved
image quality for both simulated and in-vivo datasets. Furthermore, while
reconstructions that solely use joint regularization terms are prone to
leakage-of-features, the proposed method reliably avoids leakage via
simultaneous use of joint and individual terms.
Conclusion: The proposed compressive sensing method performs fast
reconstruction of multi-channel multi-contrast MRI data with improved image
quality. It offers reliability against feature leakage in joint
reconstructions, thereby holding great promise for clinical use.Comment: 13 pages, 13 figures. Submitted for possible publicatio
PWD-3DNet: A deep learning-based fully-automated segmentation of multiple structures on temporal bone CT scans
The temporal bone is a part of the lateral skull surface that contains organs responsible for hearing and balance. Mastering surgery of the temporal bone is challenging because of this complex and microscopic three-dimensional anatomy. Segmentation of intra-temporal anatomy based on computed tomography (CT) images is necessary for applications such as surgical training and rehearsal, amongst others. However, temporal bone segmentation is challenging due to the similar intensities and complicated anatomical relationships among crit- ical structures, undetectable small structures on standard clinical CT, and the amount of time required for manual segmentation. This paper describes a single multi-class deep learning-based pipeline as the first fully automated algorithm for segmenting multiple temporal bone structures from CT volumes, including the sigmoid sinus, facial nerve, inner ear, malleus, incus, stapes, internal carotid artery and internal auditory canal. The proposed fully convolutional network, PWD-3DNet, is a patch-wise densely connected (PWD) three-dimensional (3D) network. The accuracy and speed of the proposed algorithm was shown to surpass current manual and semi-automated segmentation techniques. The experimental results yielded significantly high Dice similar- ity scores and low Hausdorff distances for all temporal bone structures with an average of 86% and 0.755 millimeter (mm), respectively. We illustrated that overlapping in the inference sub-volumes improves the segmentation performance. Moreover, we proposed augmentation layers by using samples with various transformations and image artefacts to increase the robustness of PWD-3DNet against image acquisition protocols, such as smoothing caused by soft tissue scanner settings and larger voxel sizes used for radiation reduction. The proposed algorithm was tested on low-resolution CTs acquired by another center with different scanner parameters than the ones used to create the algorithm and shows potential for application beyond the particular training data used in the study
PWD-3DNet: A Deep Learning-Based Fully-Automated Segmentation of Multiple Structures on Temporal Bone CT Scans
The temporal bone is a part of the lateral skull surface that contains organs responsible for hearing and balance. Mastering surgery of the temporal bone is challenging because of this complex and microscopic three-dimensional anatomy. Segmentation of intra-temporal anatomy based on computed tomography (CT) images is necessary for applications such as surgical training and rehearsal, amongst others. However, temporal bone segmentation is challenging due to the similar intensities and complicated anatomical relationships among critical structures, undetectable small structures on standard clinical CT, and the amount of time required for manual segmentation. This paper describes a single multi-class deep learning-based pipeline as the first fully automated algorithm for segmenting multiple temporal bone structures from CT volumes, including the sigmoid sinus, facial nerve, inner ear, malleus, incus, stapes, internal carotid artery and internal auditory canal. The proposed fully convolutional network, PWD-3DNet, is a patch-wise densely connected (PWD) three-dimensional (3D) network. The accuracy and speed of the proposed algorithm was shown to surpass current manual and semi-automated segmentation techniques. The experimental results yielded significantly high Dice similarity scores and low Hausdorff distances for all temporal bone structures with an average of 86% and 0.755 millimeter (mm), respectively. We illustrated that overlapping in the inference sub-volumes improves the segmentation performance. Moreover, we proposed augmentation layers by using samples with various transformations and image artefacts to increase the robustness of PWD-3DNet against image acquisition protocols, such as smoothing caused by soft tissue scanner settings and larger voxel sizes used for radiation reduction. The proposed algorithm was tested on low-resolution CTs acquired by another center with different scanner parameters than the ones used to create the algorithm and shows potential for application beyond the particular training data used in the study
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