Ultra-high dimensional confounder selection algorithms comparison with application to radiomics data
Radiomics is an emerging area of medical imaging data analysis particularly for cancer. It involves the conversion of digital medical images into mineable ultra-high dimensional data. Machine learning algorithms are widely used in radiomics data analysis to develop powerful decision support model to improve precision in diagnosis, assessment of prognosis and prediction of therapy response. However, machine learning algorithms for causal inference have not been previously employed in radiomics analysis. In this paper, we evaluate the value of machine learning algorithms for causal inference in radiomics. We select three recent competitive variable selection algorithms for causal inference: outcome-adaptive lasso (OAL), generalized outcome-adaptive lasso (GOAL) and causal ball screening (CBS). We used a sure independence screening procedure to propose an extension of GOAL and OAL for ultra-high dimensional data, SIS + GOAL and SIS + OAL. We compared SIS + GOAL, SIS + OAL and CBS using simulation study and two radiomics datasets in cancer, osteosarcoma and gliosarcoma. The two radiomics studies and the simulation study identified SIS + GOAL as the optimal variable selection algorithm.
相關內容
We address the communication overhead of distributed sparse matrix-(multiple)-vector multiplication in the context of large-scale eigensolvers, using filter diagonalization as an example. The basis of our study is a performance model which includes a communication metric that is computed directly from the matrix sparsity pattern without running any code. The performance model quantifies to which extent scalability and parallel efficiency are lost due to communication overhead. To restore scalability, we identify two orthogonal layers of parallelism in the filter diagonalization technique. In the horizontal layer the rows of the sparse matrix are distributed across individual processes. In the vertical layer bundles of multiple vectors are distributed across separate process groups. An analysis in terms of the communication metric predicts that scalability can be restored if, and only if, one implements the two orthogonal layers of parallelism via different distributed vector layouts. Our theoretical analysis is corroborated by benchmarks for application matrices from quantum and solid state physics, road networks, and nonlinear programming. We finally demonstrate the benefits of using orthogonal layers of parallelism with two exemplary application cases -- an exciton and a strongly correlated electron system -- which incur either small or large communication overhead.
Improving the resolution of fluorescence microscopy beyond the diffraction limit can be achievedby acquiring and processing multiple images of the sample under different illumination conditions.One of the simplest techniques, Random Illumination Microscopy (RIM), forms the super-resolvedimage from the variance of images obtained with random speckled illuminations. However, thevalidity of this process has not been fully theorized. In this work, we characterize mathematicallythe sample information contained in the variance of diffraction-limited speckled images as a functionof the statistical properties of the illuminations. We show that an unambiguous two-fold resolutiongain is obtained when the speckle correlation length coincides with the width of the observationpoint spread function. Last, we analyze the difference between the variance-based techniques usingrandom speckled illuminations (as in RIM) and those obtained using random fluorophore activation(as in Super-resolution Optical Fluctuation Imaging, SOFI).
Objective: Clinical deep phenotyping and phenotype annotation play a critical role in both the diagnosis of patients with rare disorders as well as in building computationally-tractable knowledge in the rare disorders field. These processes rely on using ontology concepts, often from the Human Phenotype Ontology, in conjunction with a phenotype concept recognition task (supported usually by machine learning methods) to curate patient profiles or existing scientific literature. With the significant shift in the use of large language models (LLMs) for most NLP tasks, we examine the performance of the latest Generative Pre-trained Transformer (GPT) models underpinning ChatGPT as a foundation for the tasks of clinical phenotyping and phenotype annotation. Materials and Methods: The experimental setup of the study included seven prompts of various levels of specificity, two GPT models (gpt-3.5-turbo and gpt-4.0) and two established gold standard corpora for phenotype recognition, one consisting of publication abstracts and the other clinical observations. Results: Our results show that, with an appropriate setup, these models can achieve state of the art performance. The best run, using few-shot learning, achieved 0.58 macro F1 score on publication abstracts and 0.75 macro F1 score on clinical observations, the former being comparable with the state of the art, while the latter surpassing the current best in class tool. Conclusion: While the results are promising, the non-deterministic nature of the outcomes, the high cost and the lack of concordance between different runs using the same prompt and input make the use of these LLMs challenging for this particular task.
Mediation analysis assesses the extent to which the exposure affects the outcome indirectly through a mediator and the extent to which it operates directly through other pathways. As the most popular method in empirical mediation analysis, the Baron-Kenny approach estimates the indirect and direct effects of the exposure on the outcome based on linear structural equation models. However, when the exposure and the mediator are not randomized, the estimates may be biased due to unmeasured confounding among the exposure, mediator, and outcome. Building on Cinelli and Hazlett (2020), we derive general omitted-variable bias formulas in linear regressions with vector responses and regressors. We then use the formulas to develop a sensitivity analysis method for the Baron-Kenny approach to mediation in the presence of unmeasured confounding. To ensure interpretability, we express the sensitivity parameters to correspond to the natural factorization of the joint distribution of the direct acyclic graph for mediation analysis. They measure the partial correlation between the unmeasured confounder and the exposure, mediator, outcome, respectively. With the sensitivity parameters, we propose a novel measure called the "robustness value for mediation" or simply the "robustness value", to assess the robustness of results based on the Baron-Kenny approach with respect to unmeasured confounding. Intuitively, the robustness value measures the minimum value of the maximum proportion of variability explained by the unmeasured confounding, for the exposure, mediator and outcome, to overturn the results of the point estimate or confidence interval for the direct and indirect effects. Importantly, we prove that all our sensitivity bounds are attainable and thus sharp.
We consider the task of estimating functions belonging to a specific class of nonsmooth functions, namely so-called tame functions. These functions appear in a wide range of applications: training deep learning, value functions of mixed-integer programs, or wave functions of small molecules. We show that tame functions are approximable by piecewise polynomials on any full-dimensional cube. We then present the first ever mixed-integer programming formulation of piecewise polynomial regression. Together, these can be used to estimate tame functions. We demonstrate promising computational results.
Magnetic Resonance Imaging (MRI) is a non-invasive diagnostic and radiotherapy (RT) planning tool, offering detailed insights into the anatomy of the human body. The extensive scan time is stressful for patients, who must remain motionless in a prolonged imaging procedure that prioritizes reduction of imaging artifacts. This is challenging for pediatric patients who may require measures for managing voluntary motions such as anesthesia. Several computational approaches reduce scan time (fast MRI), by recording fewer measurements and digitally recovering full information via post-acquisition reconstruction. However, most fast MRI approaches were developed for diagnostic imaging, without addressing reconstruction challenges specific to RT planning. In this work, we developed a deep learning-based method (DeepMRIRec) for MRI reconstruction from undersampled data acquired with RT-specific receiver coil arrangements. We evaluated our method against fully sampled data of T1-weighted MR images acquired from 73 children with brain tumors/surgical beds using loop and posterior coils (12 channels), with and without applying virtual compression of coil elements. DeepMRIRec reduced scanning time by a factor of four producing a structural similarity score surpassing the evaluated state-of-the-art method (0.960 vs 0.896), thereby demonstrating its potential for accelerating MRI scanning for RT planning.
The simulation of geological facies in an unobservable volume is essential in various geoscience applications. Given the complexity of the problem, deep generative learning is a promising approach to overcome the limitations of traditional geostatistical simulation models, in particular their lack of physical realism. This research aims to investigate the application of generative adversarial networks and deep variational inference for conditionally simulating meandering channels in underground volumes. In this paper, we review the generative deep learning approaches, in particular the adversarial ones and the stabilization techniques that aim to facilitate their training. The proposed approach is tested on 2D and 3D simulations generated by the stochastic process-based model Flumy. Morphological metrics are utilized to compare our proposed method with earlier iterations of generative adversarial networks. The results indicate that by utilizing recent stabilization techniques, generative adversarial networks can efficiently sample from target data distributions. Moreover, we demonstrate the ability to simulate conditioned simulations through the latent variable model property of the proposed approach.
This article proposes a highly accurate and conservative method for hyperbolic systems using the finite volume approach. This innovative scheme constructs the intermediate states at the interfaces of the control volumes using the method of characteristics. The approach is simple to implement, generates entropic solutions, and avoids solving Riemann problems. A diffusion control parameter is introduced to increase the accuracy of the scheme. Numerical examples are presented for the Euler equation for an ideal gas. The results demonstrate the method's ability to capture contact discontinuity and shock wave profiles with high accuracy and low cost as well as its robustness.
Robotic capacities in object manipulation are incomparable to those of humans. Besides years of learning, humans rely heavily on the richness of information from physical interaction with the environment. In particular, tactile sensing is crucial in providing such rich feedback. Despite its potential contributions to robotic manipulation, tactile sensing is less exploited; mainly due to the complexity of the time series provided by tactile sensors. In this work, we propose a method for assessing grasp stability using tactile sensing. More specifically, we propose a methodology to extract task-relevant features and design efficient classifiers to detect object slippage with respect to individual fingertips. We compare two classification models: support vector machine and logistic regression. We use highly sensitive Uskin tactile sensors mounted on an Allegro hand to test and validate our method. Our results demonstrate that the proposed method is effective in slippage detection in an online fashion.
Hashing has been widely used in approximate nearest search for large-scale database retrieval for its computation and storage efficiency. Deep hashing, which devises convolutional neural network architecture to exploit and extract the semantic information or feature of images, has received increasing attention recently. In this survey, several deep supervised hashing methods for image retrieval are evaluated and I conclude three main different directions for deep supervised hashing methods. Several comments are made at the end. Moreover, to break through the bottleneck of the existing hashing methods, I propose a Shadow Recurrent Hashing(SRH) method as a try. Specifically, I devise a CNN architecture to extract the semantic features of images and design a loss function to encourage similar images projected close. To this end, I propose a concept: shadow of the CNN output. During optimization process, the CNN output and its shadow are guiding each other so as to achieve the optimal solution as much as possible. Several experiments on dataset CIFAR-10 show the satisfying performance of SRH.
小貼士
登錄享
注冊地址： 北京市海淀區羊坊店路18號2幢3層301-191