3D mesh segmentation is an important task with many biomedical applications. The human body has bilateral symmetry and some variations in organ positions. It allows us to expect a positive effect of rotation and inversion invariant layers in convolutional neural networks that perform biomedical segmentations. In this study, we show the impact of weight symmetry in neural networks that perform 3D mesh segmentation. We analyze the problem of 3D mesh segmentation for pathological vessel structures (aneurysms) and conventional anatomical structures (endocardium and epicardium of ventricles). Local geometrical features are encoded as sampling from the signed distance function, and the neural network performs prediction for each mesh node. We show that weight symmetry gains from 1 to 3% of additional accuracy and allows decreasing the number of trainable parameters up to 8 times without suffering the performance loss if neural networks have at least three convolutional layers. This also works for very small training sets.
To form precipitation datasets that are accurate and, at the same time, have high spatial densities, data from satellites and gauges are often merged in the literature. However, uncertainty estimates for the data acquired in this manner are scarcely provided, although the importance of uncertainty quantification in predictive modelling is widely recognized. Furthermore, the benefits that machine learning can bring to the task of providing such estimates have not been broadly realized and properly explored through benchmark experiments. The present study aims at filling in this specific gap by conducting the first benchmark tests on the topic. On a large dataset that comprises 15-year-long monthly data spanning across the contiguous United States, we extensively compared six learners that are, by their construction, appropriate for predictive uncertainty quantification. These are the quantile regression (QR), quantile regression forests (QRF), generalized random forests (GRF), gradient boosting machines (GBM), light gradient boosting machines (LightGBM) and quantile regression neural networks (QRNN). The comparison referred to the competence of the learners in issuing predictive quantiles at nine levels that facilitate a good approximation of the entire predictive probability distribution, and was primarily based on the quantile and continuous ranked probability skill scores. Three types of predictor variables (i.e., satellite precipitation variables, distances between a point of interest and satellite grid points, and elevation at a point of interest) were used in the comparison and were additionally compared with each other. This additional comparison was based on the explainable machine learning concept of feature importance. The results suggest that the order from the best to the worst of the learners for the task investigated is the following: LightGBM, QRF, GRF, GBM, QRNN and QR...
Electrodermal activity (EDA) is considered a standard marker of sympathetic activity. However, traditional EDA measurement requires electrodes in steady contact with the skin. Can sympathetic arousal be measured using only an optical sensor, such as an RGB camera? This paper presents a novel approach to infer sympathetic arousal by measuring the peripheral blood flow on the face or hand optically. We contribute a self-recorded dataset of 21 participants, comprising synchronized videos of participants' faces and palms and gold-standard EDA and photoplethysmography (PPG) signals. Our results show that we can measure peripheral sympathetic responses that closely correlate with the ground truth EDA. We obtain median correlations of 0.57 to 0.63 between our inferred signals and the ground truth EDA using only videos of the participants' palms or foreheads or PPG signals from the foreheads or fingers. We also show that sympathetic arousal is best inferred from the forehead, finger, or palm.
Indolent cancers are characterized by long overall survival (OS) times. Therefore, powering a clinical trial to provide definitive assessment of the effects of an experimental intervention on OS in a reasonable timeframe is generally infeasible. Instead, the primary outcome in many pivotal trials is an intermediate clinical response such as progression-free survival (PFS). In several recently reported pivotal trials of interventions for indolent cancers that yielded promising results on an intermediate outcome, however, more mature data or post-approval trials showed concerning OS trends. These problematic results have prompted a keen interest in quantitative approaches for monitoring OS that can support regulatory decision-making related to the risk of an unacceptably large detrimental effect on OS. For example, the US Food and Drug Administration, the American Association for Cancer Research, and the American Statistical Association recently organized a one-day multi-stakeholder workshop entitled 'Overall Survival in Oncology Clinical Trials'. In this paper, we propose OS monitoring guidelines tailored for the setting of indolent cancers. Our pragmatic approach is modeled, in part, on the monitoring guidelines the FDA has used in cardiovascular safety trials conducted in Type 2 Diabetes Mellitus. We illustrate proposals through application to several examples informed by actual case studies.
The joint modeling of multiple longitudinal biomarkers together with a time-to-event outcome is a challenging modeling task of continued scientific interest. In particular, the computational complexity of high dimensional (generalized) mixed effects models often restricts the flexibility of shared parameter joint models, even when the subject-specific marker trajectories follow highly nonlinear courses. We propose a parsimonious multivariate functional principal components representation of the shared random effects. This allows better scalability, as the dimension of the random effects does not directly increase with the number of markers, only with the chosen number of principal component basis functions used in the approximation of the random effects. The functional principal component representation additionally allows to estimate highly flexible subject-specific random trajectories without parametric assumptions. The modeled trajectories can thus be distinctly different for each biomarker. We build on the framework of flexible Bayesian additive joint models implemented in the R-package 'bamlss', which also supports estimation of nonlinear covariate effects via Bayesian P-splines. The flexible yet parsimonious functional principal components basis used in the estimation of the joint model is first estimated in a preliminary step. We validate our approach in a simulation study and illustrate its advantages by analyzing a study on primary biliary cholangitis.
Multivariate spatial fields are of interest in many applications, including climate model emulation. Not only can the marginal spatial fields be subject to nonstationarity, but the dependence structure among the marginal fields and between the fields might also differ substantially. Extending a recently proposed Bayesian approach to describe the distribution of a nonstationary univariate spatial field using a triangular transport map, we cast the inference problem for a multivariate spatial field for a small number of replicates into a series of independent Gaussian process (GP) regression tasks with Gaussian errors. Due to the potential nonlinearity in the conditional means, the joint distribution modeled can be non-Gaussian. The resulting nonparametric Bayesian methodology scales well to high-dimensional spatial fields. It is especially useful when only a few training samples are available, because it employs regularization priors and quantifies uncertainty. Inference is conducted in an empirical Bayes setting by a highly scalable stochastic gradient approach. The implementation benefits from mini-batching and could be accelerated with parallel computing. We illustrate the extended transport-map model by studying hydrological variables from non-Gaussian climate-model output.
We investigate the use of multilevel Monte Carlo (MLMC) methods for estimating the expectation of discretized random fields. Specifically, we consider a setting in which the input and output vectors of the numerical simulators have inconsistent dimensions across the multilevel hierarchy. This requires the introduction of grid transfer operators borrowed from multigrid methods. Starting from a simple 1D illustration, we demonstrate numerically that the resulting MLMC estimator deteriorates the estimation of high-frequency components of the discretized expectation field compared to a Monte Carlo (MC) estimator. By adapting mathematical tools initially developed for multigrid methods, we perform a theoretical spectral analysis of the MLMC estimator of the expectation of discretized random fields, in the specific case of linear, symmetric and circulant simulators. This analysis provides a spectral decomposition of the variance into contributions associated with each scale component of the discretized field. We then propose improved MLMC estimators using a filtering mechanism similar to the smoothing process of multigrid methods. The filtering operators improve the estimation of both the small- and large-scale components of the variance, resulting in a reduction of the total variance of the estimator. These improvements are quantified for the specific class of simulators considered in our spectral analysis. The resulting filtered MLMC (F-MLMC) estimator is applied to the problem of estimating the discretized variance field of a diffusion-based covariance operator, which amounts to estimating the expectation of a discretized random field. The numerical experiments support the conclusions of the theoretical analysis even with non-linear simulators, and demonstrate the improvements brought by the proposed F-MLMC estimator compared to both a crude MC and an unfiltered MLMC estimator.
We hypothesize that due to the greedy nature of learning in multi-modal deep neural networks, these models tend to rely on just one modality while under-fitting the other modalities. Such behavior is counter-intuitive and hurts the models' generalization, as we observe empirically. To estimate the model's dependence on each modality, we compute the gain on the accuracy when the model has access to it in addition to another modality. We refer to this gain as the conditional utilization rate. In the experiments, we consistently observe an imbalance in conditional utilization rates between modalities, across multiple tasks and architectures. Since conditional utilization rate cannot be computed efficiently during training, we introduce a proxy for it based on the pace at which the model learns from each modality, which we refer to as the conditional learning speed. We propose an algorithm to balance the conditional learning speeds between modalities during training and demonstrate that it indeed addresses the issue of greedy learning. The proposed algorithm improves the model's generalization on three datasets: Colored MNIST, Princeton ModelNet40, and NVIDIA Dynamic Hand Gesture.
The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, if not better than, the original dense networks. Sparsity can reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field.
Graph representation learning for hypergraphs can be used to extract patterns among higher-order interactions that are critically important in many real world problems. Current approaches designed for hypergraphs, however, are unable to handle different types of hypergraphs and are typically not generic for various learning tasks. Indeed, models that can predict variable-sized heterogeneous hyperedges have not been available. Here we develop a new self-attention based graph neural network called Hyper-SAGNN applicable to homogeneous and heterogeneous hypergraphs with variable hyperedge sizes. We perform extensive evaluations on multiple datasets, including four benchmark network datasets and two single-cell Hi-C datasets in genomics. We demonstrate that Hyper-SAGNN significantly outperforms the state-of-the-art methods on traditional tasks while also achieving great performance on a new task called outsider identification. Hyper-SAGNN will be useful for graph representation learning to uncover complex higher-order interactions in different applications.
Radiologist is "doctor's doctor", biomedical image segmentation plays a central role in quantitative analysis, clinical diagnosis, and medical intervention. In the light of the fully convolutional networks (FCN) and U-Net, deep convolutional networks (DNNs) have made significant contributions in biomedical image segmentation applications. In this paper, based on U-Net, we propose MDUnet, a multi-scale densely connected U-net for biomedical image segmentation. we propose three different multi-scale dense connections for U shaped architectures encoder, decoder and across them. The highlights of our architecture is directly fuses the neighboring different scale feature maps from both higher layers and lower layers to strengthen feature propagation in current layer. Which can largely improves the information flow encoder, decoder and across them. Multi-scale dense connections, which means containing shorter connections between layers close to the input and output, also makes much deeper U-net possible. We adopt the optimal model based on the experiment and propose a novel Multi-scale Dense U-Net (MDU-Net) architecture with quantization. Which reduce overfitting in MDU-Net for better accuracy. We evaluate our purpose model on the MICCAI 2015 Gland Segmentation dataset (GlaS). The three multi-scale dense connections improve U-net performance by up to 1.8% on test A and 3.5% on test B in the MICCAI Gland dataset. Meanwhile the MDU-net with quantization achieves the superiority over U-Net performance by up to 3% on test A and 4.1% on test B.