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Early sensory systems in the brain rapidly adapt to fluctuating input statistics, which requires recurrent communication between neurons. Mechanistically, such recurrent communication is often indirect and mediated by local interneurons. In this work, we explore the computational benefits of mediating recurrent communication via interneurons compared with direct recurrent connections. To this end, we consider two mathematically tractable recurrent linear neural networks that statistically whiten their inputs -- one with direct recurrent connections and the other with interneurons that mediate recurrent communication. By analyzing the corresponding continuous synaptic dynamics and numerically simulating the networks, we show that the network with interneurons is more robust to initialization than the network with direct recurrent connections in the sense that the convergence time for the synaptic dynamics in the network with interneurons (resp. direct recurrent connections) scales logarithmically (resp. linearly) with the spectrum of their initialization. Our results suggest that interneurons are computationally useful for rapid adaptation to changing input statistics. Interestingly, the network with interneurons is an overparameterized solution of the whitening objective for the network with direct recurrent connections, so our results can be viewed as a recurrent linear neural network analogue of the implicit acceleration phenomenon observed in overparameterized feedforward linear neural networks.

Deep neural networks (NNs) are known for their high-prediction performances. However, NNs are prone to yield unreliable predictions when encountering completely new situations without indicating their uncertainty. Bayesian variants of NNs (BNNs), such as Monte Carlo (MC) dropout BNNs, do provide uncertainty measures and simultaneously increase the prediction performance. The only disadvantage of BNNs is their higher computation time during test time because they rely on a sampling approach. Here we present a single-shot MC dropout approximation that preserves the advantages of BNNs while being as fast as NNs. Our approach is based on moment propagation (MP) and allows to analytically approximate the expected value and the variance of the MC dropout signal for commonly used layers in NNs, i.e. convolution, max pooling, dense, softmax, and dropout layers. The MP approach can convert an NN into a BNN without re-training given the NN has been trained with standard dropout. We evaluate our approach on different benchmark datasets and a simulated toy example in a classification and regression setting. We demonstrate that our single-shot MC dropout approximation resembles the point estimate and the uncertainty estimate of the predictive distribution that is achieved with an MC approach, while being fast enough for real-time deployments of BNNs. We show that using part of the saved time to combine our MP approach with deep ensemble techniques does further improve the uncertainty measures.

Deep neural networks (DNN) are singular statistical models which exhibit complex degeneracies. In this work, we illustrate how a quantity known as the \emph{learning coefficient} introduced in singular learning theory quantifies precisely the degree of degeneracy in deep neural networks. Importantly, we will demonstrate that degeneracy in DNN cannot be accounted for by simply counting the number of "flat" directions. We propose a computationally scalable approximation of a localized version of the learning coefficient using stochastic gradient Langevin dynamics. To validate our approach, we demonstrate its accuracy in low-dimensional models with known theoretical values. Importantly, the local learning coefficient can correctly recover the ordering of degeneracy between various parameter regions of interest. An experiment on MNIST shows the local learning coefficient can reveal the inductive bias of stochastic opitmizers for more or less degenerate critical points.

Despite recent availability of large transcribed Kinyarwanda speech data, achieving robust speech recognition for Kinyarwanda is still challenging. In this work, we show that using self-supervised pre-training, following a simple curriculum schedule during fine-tuning and using semi-supervised learning to leverage large unlabelled speech data significantly improve speech recognition performance for Kinyarwanda. Our approach focuses on using public domain data only. A new studio-quality speech dataset is collected from a public website, then used to train a clean baseline model. The clean baseline model is then used to rank examples from a more diverse and noisy public dataset, defining a simple curriculum training schedule. Finally, we apply semi-supervised learning to label and learn from large unlabelled data in four successive generations. Our final model achieves 3.2% word error rate (WER) on the new dataset and 15.9% WER on Mozilla Common Voice benchmark, which is state-of-the-art to the best of our knowledge. Our experiments also indicate that using syllabic rather than character-based tokenization results in better speech recognition performance for Kinyarwanda.

In the past decades, automated high-content microscopy demonstrated its ability to deliver large quantities of image-based data powering the versatility of phenotypic drug screening and systems biology applications. However, as the sizes of image-based datasets grew, it became infeasible for humans to control, avoid and overcome the presence of imaging and sample preparation artefacts in the images. While novel techniques like machine learning and deep learning may address these shortcomings through generative image inpainting, when applied to sensitive research data this may come at the cost of undesired image manipulation. Undesired manipulation may be caused by phenomena such as neural hallucinations, to which some artificial neural networks are prone. To address this, here we evaluate the state-of-the-art inpainting methods for image restoration in a high-content fluorescence microscopy dataset of cultured cells with labelled nuclei. We show that architectures like DeepFill V2 and Edge Connect can faithfully restore microscopy images upon fine-tuning with relatively little data. Our results demonstrate that the area of the region to be restored is of higher importance than shape. Furthermore, to control for the quality of restoration, we propose a novel phenotype-preserving metric design strategy. In this strategy, the size and count of the restored biological phenotypes like cell nuclei are quantified to penalise undesirable manipulation. We argue that the design principles of our approach may also generalise to other applications.

High-level synthesis (HLS) refers to the automatic translation of a software program written in a high-level language into a hardware design. Modern HLS tools have moved away from the traditional approach of static (compile time) scheduling of operations to generating dynamic circuits that schedule operations at run time. Such circuits trade-off area utilisation for increased dynamism and throughput. However, existing lowering flows in dynamically scheduled HLS tools rely on conservative assumptions on their input program due to both the intermediate representations (IR) utilised as well as the lack of formal specifications on the translation into hardware. These assumptions cause suboptimal hardware performance. In this work, we lift these assumptions by proposing a new and efficient abstraction for hardware mapping; namely h-GSA, an extension of the Gated Single Static Assignment (GSA) IR. Using this abstraction, we propose a lowering flow that transforms GSA into h-GSA and maps h-GSA into dynamically scheduled hardware circuits. We compare the schedules generated by our approach to those by the state-of-the-art dynamic-scheduling HLS tool, Dynamatic, and illustrate the potential performance improvement from hardware mapping using the proposed abstraction.

We present ResMLP, an architecture built entirely upon multi-layer perceptrons for image classification. It is a simple residual network that alternates (i) a linear layer in which image patches interact, independently and identically across channels, and (ii) a two-layer feed-forward network in which channels interact independently per patch. When trained with a modern training strategy using heavy data-augmentation and optionally distillation, it attains surprisingly good accuracy/complexity trade-offs on ImageNet. We will share our code based on the Timm library and pre-trained models.

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.

Recent advances in 3D fully convolutional networks (FCN) have made it feasible to produce dense voxel-wise predictions of volumetric images. In this work, we show that a multi-class 3D FCN trained on manually labeled CT scans of several anatomical structures (ranging from the large organs to thin vessels) can achieve competitive segmentation results, while avoiding the need for handcrafting features or training class-specific models. To this end, we propose a two-stage, coarse-to-fine approach that will first use a 3D FCN to roughly define a candidate region, which will then be used as input to a second 3D FCN. This reduces the number of voxels the second FCN has to classify to ~10% and allows it to focus on more detailed segmentation of the organs and vessels. We utilize training and validation sets consisting of 331 clinical CT images and test our models on a completely unseen data collection acquired at a different hospital that includes 150 CT scans, targeting three anatomical organs (liver, spleen, and pancreas). In challenging organs such as the pancreas, our cascaded approach improves the mean Dice score from 68.5 to 82.2%, achieving the highest reported average score on this dataset. We compare with a 2D FCN method on a separate dataset of 240 CT scans with 18 classes and achieve a significantly higher performance in small organs and vessels. Furthermore, we explore fine-tuning our models to different datasets. Our experiments illustrate the promise and robustness of current 3D FCN based semantic segmentation of medical images, achieving state-of-the-art results. Our code and trained models are available for download: //github.com/holgerroth/3Dunet_abdomen_cascade.