Semantic Segmentation using Neural Ordinary Differential Equations

The idea of neural Ordinary Differential Equations (ODE) is to approximate the derivative of a function (data model) instead of the function itself. In residual networks, instead of having a discrete sequence of hidden layers, the derivative of the continuous dynamics of hidden state can be parameterized by an ODE. It has been shown that this type of neural network is able to produce the same results as an equivalent residual network for image classification. In this paper, we design a novel neural ODE for the semantic segmentation task. We start by a baseline network that consists of residual modules, then we use the modules to build our neural ODE network. We show that our neural ODE is able to achieve the state-of-the-art results using 57% less memory for training, 42% less memory for testing, and 68% less number of parameters. We evaluate our model on the Cityscapes, CamVid, LIP, and PASCAL-Context datasets

Local Neighborhood Features for 3D Classification

With advances in deep learning model training strategies, the training of Point cloud classification methods is significantly improving. For example, PointNeXt, which adopts prominent training techniques and InvResNet layers into PointNet++, achieves over 7% improvement on the real-world ScanObjectNN dataset. However, most of these models use point coordinates features of neighborhood points mapped to higher dimensional space while ignoring the neighborhood point features computed before feeding to the network layers. In this paper, we revisit the PointNeXt model to study the usage and benefit of such neighborhood point features. We train and evaluate PointNeXt on ModelNet40 (synthetic), ScanObjectNN (real-world), and a recent large-scale, real-world grocery dataset, i.e., 3DGrocery100. In addition, we provide an additional inference strategy of weight averaging the top two checkpoints of PointNeXt to improve classification accuracy. Together with the abovementioned ideas, we gain 0.5%, 1%, 4.8%, 3.4%, and 1.6% overall accuracy on the PointNeXt model with real-world datasets, ScanObjectNN (hardest variant), 3DGrocery100's Apple10, Fruits, Vegetables, and Packages subsets, respectively. We also achieve a comparable 0.2% accuracy gain on ModelNet40

CIS UDEL Working Notes on ImageCLEF 2015: Compound figure detection task

Abstract. Figures that are included in biomedical publications play an important role in understanding essential aspects of the paper. Much work over the past few years has focused on figure analysis and classification in biomedical documents. As many of the figures appearing in biomedical documents comprise multiple panels (subfigures), the first step in the analysis requires identification of compound figures and their segmentation into subfigures. There is a wide variety ways to detect compound figures. In this paper, we utilize only visual information to identify compound vs non-compound figures. We have tested the proposed approach on the ImageCLEF 2015 benchmark of 10, 434 images; our approach has achieved an accuracy of 82.82%, thus demonstrating the best performance when compared to other systems that use only visual information for addressing the compound figure detection task

Stromule extension along microtubules coordinated with actin-mediated anchoring guides perinuclear chloroplast movement during innate immunity.

Dynamic tubular extensions from chloroplasts called stromules have recently been shown to connect with nuclei and function during innate immunity. We demonstrate that stromules extend along microtubules (MTs) and MT organization directly affects stromule dynamics since stabilization of MTs chemically or genetically increases stromule numbers and length. Although actin filaments (AFs) are not required for stromule extension, they provide anchor points for stromules. Interestingly, there is a strong correlation between the direction of stromules from chloroplasts and the direction of chloroplast movement. Stromule-directed chloroplast movement was observed in steady-state conditions without immune induction, suggesting it is a general function of stromules in epidermal cells. Our results show that MTs and AFs may facilitate perinuclear clustering of chloroplasts during an innate immune response. We propose a model in which stromules extend along MTs and connect to AF anchor points surrounding nuclei, facilitating stromule-directed movement of chloroplasts to nuclei during innate immunity

Towards an Integrated Multiscale Simulation of Turbulent Clouds on PetaScale Computers

The development of precipitating warm clouds is affected by several effects of small-scale air turbulence including enhancement of droplet-droplet collision rate by turbulence, entrainment and mixing at the cloud edges, and coupling of mechanical and thermal energies at various scales. Large-scale computation is a viable research tool for quantifying these multiscale processes. Specifically, top-down large-eddy simulations (LES) of shallow convective clouds typically resolve scales of turbulent energy-containing eddies while the effects of turbulent cascade toward viscous dissipation are parameterized. Bottom-up hybrid direct numerical simulations (HDNS) of cloud microphysical processes resolve fully the dissipation-range flow scales but only partially the inertial subrange scales. it is desirable to systematically decrease the grid length in LES and increase the domain size in HDNS so that they can be better integrated to address the full range of scales and their coupling. In this paper, we discuss computational issues and physical modeling questions in expanding the ranges of scales realizable in LES and HDNS, and in bridging LES and HDNS. We review our on-going efforts in transforming our simulation codes towards PetaScale computing, in improving physical representations in LES and HDNS, and in developing better methods to analyze and interpret the simulation results