A tensor-based population value decomposition to explain rectal toxicity after prostate cancer radiotherapy.
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ABSTRACT:
SUBMITTER: Ospina JD
PROVIDER: S-EPMC3970197 | biostudies-literature | 2013
REPOSITORIES: biostudies-literature
Publications
A tensor-based population value decomposition to explain rectal toxicity after prostate cancer radiotherapy.
Ospina Juan David JD Commandeur Frédéric F Ríos Richard R Dréan Gaël G Correa Juan Carlos JC Simon Antoine A Haigron Pascal P de Crevoisier Renaud R Acosta Oscar O
Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 20130101 Pt 2
In prostate cancer radiotherapy the association between the dose distribution and the occurrence of undesirable side-effects is yet to be revealed. In this work a method to perform population analysis by comparing the dose distributions is proposed. The method is a tensor-based approach that generalises an existing method for 2D images and allows for the highlighting of over irradiated zones correlated with rectal bleeding after prostate cancer radiotherapy. Thus, the aim is to contribute to the ...[more]
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Project description:Background and purposeAssociations between dose and rectal toxicity in prostate radiotherapy are generally poorly understood. Evaluating spatial dose distributions to the rectal wall (RW) may lead to improvements in dose-toxicity modelling by incorporating geometric information, masked by dose-volume histograms. Furthermore, predictive power may be strengthened by incorporating the effects of interfraction motion into delivered dose calculations.Here we interrogate 3D dose distributions for patients with and without toxicity to identify rectal subregions at risk (SRR), and compare the discriminatory ability of planned and delivered dose.Material and methodsDaily delivered dose to the rectum was calculated using image guidance scans, and accumulated at the voxel level using biomechanical finite element modelling. SRRs were statistically determined for rectal bleeding, proctitis, faecal incontinence and stool frequency from a training set (n = 139), and tested on a validation set (n = 47).ResultsSRR patterns differed per endpoint. Analysing dose to SRRs improved discriminative ability with respect to the full RW for three of four endpoints. Training set AUC and OR analysis produced stronger toxicity associations from accumulated dose than planned dose. For rectal bleeding in particular, accumulated dose to the SRR (AUC 0.76) improved upon dose-toxicity associations derived from planned dose to the RW (AUC 0.63). However, validation results could not be considered significant.ConclusionsVoxel-level analysis of dose to the RW revealed SRRs associated with rectal toxicity, suggesting non-homogeneous intra-organ radiosensitivity. Incorporating spatial features of accumulated delivered dose improved dose-toxicity associations. This may be an important tool for adaptive radiotherapy in the future.
| S-EPMC7301619 | biostudies-literature
Project description:The large p small n problem is a challenge without a de facto standard method available to it. In this study, we propose a tensor-decomposition (TD)-based unsupervised feature extraction (FE) formalism applied to multiomics datasets, in which the number of features is more than 100,000 whereas the number of samples is as small as about 100, hence constituting a typical large p small n problem. The proposed TD-based unsupervised FE outperformed other conventional supervised feature selection methods, random forest, categorical regression (also known as analysis of variance, or ANOVA), penalized linear discriminant analysis, and two unsupervised methods, multiple non-negative matrix factorization and principal component analysis (PCA) based unsupervised FE when applied to synthetic datasets and four methods other than PCA based unsupervised FE when applied to multiomics datasets. The genes selected by TD-based unsupervised FE were enriched in genes known to be related to tissues and transcription factors measured. TD-based unsupervised FE was demonstrated to be not only the superior feature selection method but also the method that can select biologically reliable genes. To our knowledge, this is the first study in which TD-based unsupervised FE has been successfully applied to the integration of this variety of multiomics measurements.
| S-EPMC7763286 | biostudies-literature
Project description:Background: A rectal sub-region (SRR) has been previously identified by voxel-wise analysis in the inferior-anterior part of the rectum as highly predictive of rectal bleeding (RB) in prostate cancer radiotherapy. Translating the SRR to patient-specific radiotherapy planning is challenging as new constraints have to be defined. A recent geometry-based model proposed to optimize the planning by determining the achievable mean doses (AMDs) to the organs at risk (OARs), taking into account the overlap between the planning target volume (PTV) and OAR. The aim of this study was to quantify the SRR dose sparing by using the AMD model in the planning, while preserving the dose to the prostate. Material and Methods: Three-dimensional volumetric modulated arc therapy (VMAT) planning dose distributions for 60 patients were computed following four different strategies, delivering 78 Gy to the prostate, while meeting the genitourinary group dose constraints to the OAR: (i) a standard plan corresponding to the standard practice for rectum sparing (STDpl), (ii) a plan adding constraints to SRR (SRRpl), (iii) a plan using the AMD model applied to the rectum only (AMD_RECTpl), and (iv) a final plan using the AMD model applied to both the rectum and the SRR (AMD_RECT_SRRpl). After PTV dose normalization, plans were compared with regard to dose distributions, quality, and estimated risk of RB using a normal tissue complication probability model. Results: AMD_RECT_SRRpl showed the largest SRR dose sparing, with significant mean dose reductions of 7.7, 3, and 2.3 Gy, with respect to the STDpl, SRRpl, and AMD_RECTpl, respectively. AMD_RECT_SRRpl also decreased the mean rectal dose by 3.6 Gy relative to STDpl and by 3.3 Gy relative to SRRpl. The absolute risk of grade ≥1 RB decreased from 22.8% using STDpl planning to 17.6% using AMD_RECT_SRRpl considering SRR volume. AMD_RECT_SRRpl plans, however, showed slightly less dose homogeneity and significant increase of the number of monitor units, compared to the three other strategies. Conclusion: Compared to a standard prostate planning, applying dose constraints to a patient-specific SRR by using the achievable mean dose model decreased the mean dose by 7.7 Gy to the SRR and may decrease the relative risk of RB by 22%.
| S-EPMC7517942 | biostudies-literature
Project description:Background and purposeFor the first time, delivered dose to the rectum has been calculated and accumulated throughout the course of prostate radiotherapy using megavoltage computed tomography (MVCT) image guidance scans. Dosimetric parameters were linked with toxicity to test the hypothesis that delivered dose is a stronger predictor of toxicity than planned dose.Material and methodsDose-surface maps (DSMs) of the rectal wall were automatically generated from daily MVCT scans for 109 patients within the VoxTox research programme. Accumulated-DSMs, representing total delivered dose, and planned-DSMs, from planning CT data, were parametrised using Equivalent Uniform Dose (EUD) and 'DSM dose-width', the lateral dimension of an ellipse fitted to a discrete isodose cluster. Associations with 6 toxicity endpoints were assessed using receiver operator characteristic curve analysis.ResultsFor rectal bleeding, the area under the curve (AUC) was greater for accumulated dose than planned dose for DSM dose-widths up to 70Gy. Accumulated 65Gy DSM dose-width produced the strongest spatial correlation (AUC 0.664), while accumulated EUD generated the largest AUC overall (0.682). For proctitis, accumulated EUD was the only reportable predictor (AUC 0.673). Accumulated EUD was systematically lower than planned EUD.ConclusionsDosimetric parameters extracted from accumulated DSMs have demonstrated stronger correlations with rectal bleeding and proctitis, than planned DSMs.
| S-EPMC5486775 | biostudies-literature
Project description:Single-cell multi-omics refers to the various types of biological data at the single-cell level. These data have enabled insight and resolution to cellular phenotypes, biological processes, and developmental stages. Current advances hold high potential for breakthroughs by integrating multiple different omics layers. However, singlecell multi-omics data usually have different feature dimensions and direct or indirect relationships. How to keep the data structure of these different data and extract hidden relationships is a major challenge for omics data integration, and effective integration models are urgently needed. In this paper, we propose an irregular tensor decomposition model (GSTRPCA) based on tensor robust principal component analysis (TRPCA). We developed a weighted threshold model for the decomposition of irregular tensor data by combining low-rank and sparsity constraints, which requires that the low-dimensional embeddings of the data remain lowrank and sparse. The major advantage of the GSTRPCA algorithm is its ability to keep the original data structure and explore hidden related features among omics data. For GSTRPCA, we also designed an effective algorithm that theoretically guarantees global convergence for the tensor decomposition. The computational experiments on irregular tensor datasets demonstrate that GSTRPCA significantly outperformed the state-of-the-art methods and hence confirm the superiority of GSTRPCA in clustering single-cell multiomics data. To our knowledge, this is the first tensor decomposition method for irregular tensor data to keep the data structure and hence improve the clustering performance for single-cell multi-omics data. GSTRPCA is a Matlabbased algorithm, and the code is available from https://github.com/GGL-B/GSTRPCA.
| S-EPMC11647523 | biostudies-literature
Project description:The Encyclopedia of DNA Elements (ENCODE) and the Roadmap Epigenomics Project seek to characterize the epigenome in diverse cell types using assays that identify, for example, genomic regions with modified histones or accessible chromatin. These efforts have produced thousands of datasets but cannot possibly measure each epigenomic factor in all cell types. To address this, we present a method, PaRallel Epigenomics Data Imputation with Cloud-based Tensor Decomposition (PREDICTD), to computationally impute missing experiments. PREDICTD leverages an elegant model called "tensor decomposition" to impute many experiments simultaneously. Compared with the current state-of-the-art method, ChromImpute, PREDICTD produces lower overall mean squared error, and combining the two methods yields further improvement. We show that PREDICTD data captures enhancer activity at noncoding human accelerated regions. PREDICTD provides reference imputed data and open-source software for investigating new cell types, and demonstrates the utility of tensor decomposition and cloud computing, both promising technologies for bioinformatics.
| S-EPMC5895786 | biostudies-literature
Project description:BackgroundBetter knowledge of the dose-toxicity relationship is essential for safe dose escalation to improve local control in cervical cancer radiotherapy. The conventional dose-toxicity model is based on the dose volume histogram, which is the parameter lacking spatial dose information. To overcome this limit, we explore a comprehensive rectal dose-toxicity model based on both dose volume histogram and dose map features for accurate radiation toxicity prediction.MethodsForty-two cervical cancer patients treated with combined external beam radiotherapy (EBRT) and brachytherapy (BT) were retrospectively studied, including 12 with Grade ≥ 2 rectum toxicity and 30 patients with Grade 0-1 toxicity (non-toxicity patients). The cumulative equivalent 2-Gy rectal surface dose was deformably summed using the deformation vector fields obtained through a recent developed local topology preserved non-rigid point matching algorithm. The cumulative three-dimensional (3D) dose was flattened and mapped to a two-dimensional (2D) plane to obtain the rectum surface dose map (RSDM). The dose volume parameters (DVPs) were calculated from the 3D rectum surface, while the texture features and the dose geometric parameters (DGPs) were extracted from the 2D RSDM. Representative features further computed from DVPs, textures and DGPs by principle component analysis (PCA) and statistical analysis were respectively fed into a support vector machine equipped with a sequential feature selection procedure. The predictive powers of the representative features were compared with the GEC-ESTRO dosimetric parameters D0.1/1/2cm3.ResultsSatisfactory predictive accuracy of sensitivity 74.75 and 84.75%, specificity 72.67 and 79.87%, and area under the receiver operating characteristic curve (AUC) 0.82 and 0.91 were respectively achieved by the PCA features and statistical significant features, which were superior to the D0.1/1/2cm3 (AUC 0.71). The relative area in dose levels of 64Gy, 67Gy, 68Gy, 87Gy, 88Gy and 89Gy, perimeters in dose levels of 89Gy, as well as two texture features were ranked as the important factors that were closely correlated with rectal toxicity.ConclusionsOur extensive experimental results have demonstrated the feasibility of the proposed scheme. A future large patient cohort study is still needed for model validation.
| S-EPMC6035458 | biostudies-literature
Project description:BackgroundThere is a lack of comprehensive reports on time trends in synchronous prostate and rectal cancers. To address this, we conducted the largest cohort study to date to assess these trends in a population-based setting.MethodsWe included all adult (ages 18-99) men with incident prostate cancer in the Swedish Cancer Register in 1993-2019. Age-standardized incidence rates (ASIRs) of prostate cancer per 100,000 male population per year were calculated and compared to the ASIR of synchronous (± 6 months from rectal cancer diagnosis) prostate cancer. Age-adjusted synchronous-to-general incidence rate ratios (IRRs) were predicted using Poisson regression. As a sensitivity analysis to assess the effect of incidental findings due to the anatomical proximity, we investigated synchronous prostate and non-sigmoid colon cancers.ResultsAmong 238,252 prostate cancer cases, 594 were synchronous with rectal cancer. The incidence of synchronous prostate cancer increased over the study period, with mean ASIR rising from 418/100,000 (1993-2001) to 788/100,000 (year 2011-2019). The synchronous-to-general IRR increased from 1.92 (95% confidence interval (CI) 1.60-2.31) to 2.61 (95% CI 2.32-2.95) over the same periods. Prostate cancer was also more commonly diagnosed in conjunction with non-sigmoid colon cancer than in the overall male population, but no time trend was observed.InterpretationThe incidence of synchronous prostate and rectal cancers has increased over the past 20 years in Sweden, with no signs of plateauing. Future studies are warranted to explore factors contributing to prostate cancer overdiagnosis and to optimize clinical management strategies for this complex patient group.
| S-EPMC11905149 | biostudies-literature
Project description:Hypergraphs have gained increasing attention in the machine learning community lately due to their superiority over graphs in capturing super-dyadic interactions among entities. In this work, we propose a novel approach for the partitioning of k-uniform hypergraphs. Most of the existing methods work by reducing the hypergraph to a graph followed by applying standard graph partitioning algorithms. The reduction step restricts the algorithms to capturing only some weighted pairwise interactions and hence loses essential information about the original hypergraph. We overcome this issue by utilizing tensor-based representation of hypergraphs, which enables us to capture actual super-dyadic interactions. We extend the notion of minimum ratio-cut and normalized-cut from graphs to hypergraphs and show that the relaxed optimization problem can be solved using eigenvalue decomposition of the Laplacian tensor. This novel formulation also enables us to remove a hyperedge completely by using the "hyperedge score" metric proposed by us, unlike the existing reduction approaches. We propose a hypergraph partitioning algorithm inspired from spectral graph theory and also derive a tighter upper bound on the minimum positive eigenvalue of even-order hypergraph Laplacian tensor in terms of its conductance, which is utilized in the partitioning algorithm to approximate the normalized cut. The efficacy of the proposed method is demonstrated numerically on synthetic hypergraphs generated by stochastic block model. We also show improvement for the min-cut solution on 2-uniform hypergraphs (graphs) over the standard spectral partitioning algorithm.
| S-EPMC10361499 | biostudies-literature
Project description:Analysis of single-cell multiomics datasets is a novel topic and is considerably challenging because such datasets contain a large number of features with numerous missing values. In this study, we implemented a recently proposed tensor-decomposition (TD)-based unsupervised feature extraction (FE) technique to address this difficult problem. The technique can successfully integrate single-cell multiomics data composed of gene expression, DNA methylation, and accessibility. Although the last two have large dimensions, as many as ten million, containing only a few percentage of nonzero values, TD-based unsupervised FE can integrate three omics datasets without filling in missing values. Together with UMAP, which is used frequently when embedding single-cell measurements into two-dimensional space, TD-based unsupervised FE can produce two-dimensional embedding coincident with classification when integrating single-cell omics datasets. Genes selected based on TD-based unsupervised FE are also significantly related to reasonable biological roles.
| S-EPMC8468466 | biostudies-literature