Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the measurement of gene expressions at the single cell level along with the spatial locations of these cells in the tissue. Dimension-reduction and spatial clustering are two of the most common exploratory analysis strategies for spatial transcriptomic data. However, existing dimension reduction methods may lead to a loss of inherent dependency structure among genes at any spatial location in the tissue and hence do not provide insights of gene co-expression pattern. In spatial transcriptomics, the matrix-variate gene expression data, along with spatial co-ordinates of the single cells, provides information on both gene expression dependencies and cell spatial dependencies through its row and column covariances. In this work, we propose a flexible Bayesian approach to simultaneously estimate the row and column covariances for the matrix-variate spatial transcriptomic data. The posterior estimates of the row and column covariances provide data summaries for downstream exploratory analysis. We illustrate our method with simulations and two analyses of real data generated from a recent spatial transcriptomic platform. Our work elucidates gene co-expression networks as well as clear spatial clustering patterns of the cells.
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Numerical simulations of high energy-density experiments require equation of state (EOS) models that relate a material's thermodynamic state variables -- specifically pressure, volume/density, energy, and temperature. EOS models are typically constructed using a semi-empirical parametric methodology, which assumes a physics-informed functional form with many tunable parameters calibrated using experimental/simulation data. Since there are inherent uncertainties in the calibration data (parametric uncertainty) and the assumed functional EOS form (model uncertainty), it is essential to perform uncertainty quantification (UQ) to improve confidence in the EOS predictions. Model uncertainty is challenging for UQ studies since it requires exploring the space of all possible physically consistent functional forms. Thus, it is often neglected in favor of parametric uncertainty, which is easier to quantify without violating thermodynamic laws. This work presents a data-driven machine learning approach to constructing EOS models that naturally captures model uncertainty while satisfying the necessary thermodynamic consistency and stability constraints. We propose a novel framework based on physics-informed Gaussian process regression (GPR) that automatically captures total uncertainty in the EOS and can be jointly trained on both simulation and experimental data sources. A GPR model for the shock Hugoniot is derived and its uncertainties are quantified using the proposed framework. We apply the proposed model to learn the EOS for the diamond solid state of carbon, using both density functional theory data and experimental shock Hugoniot data to train the model and show that the prediction uncertainty reduces by considering the thermodynamic constraints.
Given the high incidence of cardio and cerebrovascular diseases (CVD), and its association with morbidity and mortality, its prevention is a major public health issue. A high level of blood pressure is a well-known risk factor for these events and an increasing number of studies suggest that blood pressure variability may also be an independent risk factor. However, these studies suffer from significant methodological weaknesses. In this work we propose a new location-scale joint model for the repeated measures of a marker and competing events. This joint model combines a mixed model including a subject-specific and time-dependent residual variance modeled through random effects, and cause-specific proportional intensity models for the competing events. The risk of events may depend simultaneously on the current value of the variance, as well as, the current value and the current slope of the marker trajectory. The model is estimated by maximizing the likelihood function using the Marquardt-Levenberg algorithm. The estimation procedure is implemented in a R-package and is validated through a simulation study. This model is applied to study the association between blood pressure variability and the risk of CVD and death from other causes. Using data from a large clinical trial on the secondary prevention of stroke, we find that the current individual variability of blood pressure is associated with the risk of CVD and death. Moreover, the comparison with a model without heterogeneous variance shows the importance of taking into account this variability in the goodness-of-fit and for dynamic predictions.
This article shows how to develop an efficient solver for a stabilized numerical space-time formulation of the advection-dominated diffusion transient equation. At the discrete space-time level, we approximate the solution by using higher-order continuous B-spline basis functions in its spatial and temporal dimensions. This problem is very difficult to solve numerically using the standard Galerkin finite element method due to artificial oscillations present when the advection term dominates the diffusion term. However, a first-order constraint least-square formulation allows us to obtain numerical solutions avoiding oscillations. The advantages of space-time formulations are the use of high-order methods and the feasibility of developing space-time mesh adaptive techniques on well-defined discrete problems. We develop a solver for a least-square formulation to obtain a stabilized and symmetric problem on finite element meshes. The computational cost of our solver is bounded by the cost of the inversion of the space-time mass and stiffness (with one value fixed at a point) matrices and the cost of the GMRES solver applied for the symmetric and positive definite problem. We illustrate our findings on an advection-dominated diffusion space-time model problem and present two numerical examples: one with isogeometric analysis discretizations and the second one with an adaptive space-time finite element method.
Recurrent Neural Networks (RNNs) are frequently used to model aspects of brain function and structure. In this work, we trained small fully-connected RNNs to perform temporal and flow control tasks with time-varying stimuli. Our results show that different RNNs can solve the same task by converging to different underlying dynamics and also how the performance gracefully degrades as either network size is decreased, interval duration is increased, or connectivity damage is increased. For the considered tasks, we explored how robust the network obtained after training can be according to task parameterization. In the process, we developed a framework that can be useful to parameterize other tasks of interest in computational neuroscience. Our results are useful to quantify different aspects of the models, which are normally used as black boxes and need to be understood in order to model the biological response of cerebral cortex areas.
In this paper, we explore the new design space of extra-linguistic cues inspired by graphical tropes used in graphic novels and animation to enhance the expressiveness of social robots. To achieve this, we identified a set of cues that can be used to generate expressions, including smoke/steam/fog, water droplets, and bubbles. We prototyped devices that can generate these fluid expressions for a robot and conducted design sessions where eight designers explored the use and utility of the cues in conveying the robot's internal states in various design scenarios. Our analysis of the 22 designs, the associated design justifications, and the interviews with designers revealed patterns in how each cue was used, how they were combined with nonverbal cues, and where the participants drew their inspiration from. These findings informed the design of an integrated module called EmoPack, which can be used to augment the expressive capabilities of any robot platform.
Recurrent neural network-based reinforcement learning systems are capable of complex motor control tasks such as locomotion and manipulation, however, much of their underlying mechanisms still remain difficult to interpret. Our aim is to leverage computational neuroscience methodologies to understanding the population-level activity of robust robot locomotion controllers. Our investigation begins by analyzing topological structure, discovering that fragile controllers have a higher number of fixed points with unstable directions, resulting in poorer balance when instructed to stand in place. Next, we analyze the forced response of the system by applying targeted neural perturbations along directions of dominant population-level activity. We find evidence that recurrent state dynamics are structured and low-dimensional during walking, which aligns with primate studies. Additionally, when recurrent states are perturbed to zero, fragile agents continue to walk, which is indicative of a stronger reliance on sensory input and weaker recurrence.
Training nonlinear parametrizations such as deep neural networks to numerically approximate solutions of partial differential equations is often based on minimizing a loss that includes the residual, which is analytically available in limited settings only. At the same time, empirically estimating the training loss is challenging because residuals and related quantities can have high variance, especially for transport-dominated and high-dimensional problems that exhibit local features such as waves and coherent structures. Thus, estimators based on data samples from un-informed, uniform distributions are inefficient. This work introduces Neural Galerkin schemes that estimate the training loss with data from adaptive distributions, which are empirically represented via ensembles of particles. The ensembles are actively adapted by evolving the particles with dynamics coupled to the nonlinear parametrizations of the solution fields so that the ensembles remain informative for estimating the training loss. Numerical experiments indicate that few dynamic particles are sufficient for obtaining accurate empirical estimates of the training loss, even for problems with local features and with high-dimensional spatial domains.
Deep learning has shown great potential for modeling the physical dynamics of complex particle systems such as fluids (in Lagrangian descriptions). Existing approaches, however, require the supervision of consecutive particle properties, including positions and velocities. In this paper, we consider a partially observable scenario known as fluid dynamics grounding, that is, inferring the state transitions and interactions within the fluid particle systems from sequential visual observations of the fluid surface. We propose a differentiable two-stage network named NeuroFluid. Our approach consists of (i) a particle-driven neural renderer, which involves fluid physical properties into the volume rendering function, and (ii) a particle transition model optimized to reduce the differences between the rendered and the observed images. NeuroFluid provides the first solution to unsupervised learning of particle-based fluid dynamics by training these two models jointly. It is shown to reasonably estimate the underlying physics of fluids with different initial shapes, viscosity, and densities. It is a potential alternative approach to understanding complex fluid mechanics, such as turbulence, that are difficult to model using traditional methods of mathematical physics.
As soon as abstract mathematical computations were adapted to computation on digital computers, the problem of efficient representation, manipulation, and communication of the numerical values in those computations arose. Strongly related to the problem of numerical representation is the problem of quantization: in what manner should a set of continuous real-valued numbers be distributed over a fixed discrete set of numbers to minimize the number of bits required and also to maximize the accuracy of the attendant computations? This perennial problem of quantization is particularly relevant whenever memory and/or computational resources are severely restricted, and it has come to the forefront in recent years due to the remarkable performance of Neural Network models in computer vision, natural language processing, and related areas. Moving from floating-point representations to low-precision fixed integer values represented in four bits or less holds the potential to reduce the memory footprint and latency by a factor of 16x; and, in fact, reductions of 4x to 8x are often realized in practice in these applications. Thus, it is not surprising that quantization has emerged recently as an important and very active sub-area of research in the efficient implementation of computations associated with Neural Networks. In this article, we survey approaches to the problem of quantizing the numerical values in deep Neural Network computations, covering the advantages/disadvantages of current methods. With this survey and its organization, we hope to have presented a useful snapshot of the current research in quantization for Neural Networks and to have given an intelligent organization to ease the evaluation of future research in this area.
Self-supervised learning has been widely used to obtain transferrable representations from unlabeled images. Especially, recent contrastive learning methods have shown impressive performances on downstream image classification tasks. While these contrastive methods mainly focus on generating invariant global representations at the image-level under semantic-preserving transformations, they are prone to overlook spatial consistency of local representations and therefore have a limitation in pretraining for localization tasks such as object detection and instance segmentation. Moreover, aggressively cropped views used in existing contrastive methods can minimize representation distances between the semantically different regions of a single image. In this paper, we propose a spatially consistent representation learning algorithm (SCRL) for multi-object and location-specific tasks. In particular, we devise a novel self-supervised objective that tries to produce coherent spatial representations of a randomly cropped local region according to geometric translations and zooming operations. On various downstream localization tasks with benchmark datasets, the proposed SCRL shows significant performance improvements over the image-level supervised pretraining as well as the state-of-the-art self-supervised learning methods.
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