In recent years, deep learning has been a topic of interest in almost all disciplines due to its impressive empirical success in analyzing complex data sets, such as imaging, genetics, climate, and medical data. While most of the developments are treated as black-box machines, there is an increasing interest in interpretable, reliable, and robust deep learning models applicable to a broad class of applications. Feature-selected deep learning is proven to be promising in this regard. However, the recent developments do not address the situations of ultra-high dimensional and highly correlated feature selection in addition to the high noise level. In this article, we propose a novel screening and cleaning strategy with the aid of deep learning for the cluster-level discovery of highly correlated predictors with a controlled error rate. A thorough empirical evaluation over a wide range of simulated scenarios demonstrates the effectiveness of the proposed method by achieving high power while having a minimal number of false discoveries. Furthermore, we implemented the algorithm in the riboflavin (vitamin $B_2$) production dataset in the context of understanding the possible genetic association with riboflavin production. The gain of the proposed methodology is illustrated by achieving lower prediction error compared to other state-of-the-art methods.
相關內容
Dimensionality reduction techniques aim at representing high-dimensional data in low-dimensional spaces to extract hidden and useful information or facilitate visual understanding and interpretation of the data. However, few of them take into consideration the potential cluster information contained implicitly in the high-dimensional data. In this paper, we propose LaptSNE, a new graph-layout nonlinear dimensionality reduction method based on t-SNE, one of the best techniques for visualizing high-dimensional data as 2D scatter plots. Specifically, LaptSNE leverages the eigenvalue information of the graph Laplacian to shrink the potential clusters in the low-dimensional embedding when learning to preserve the local and global structure from high-dimensional space to low-dimensional space. It is nontrivial to solve the proposed model because the eigenvalues of normalized symmetric Laplacian are functions of the decision variable. We provide a majorization-minimization algorithm with convergence guarantee to solve the optimization problem of LaptSNE and show how to calculate the gradient analytically, which may be of broad interest when considering optimization with Laplacian-composited objective. We evaluate our method by a formal comparison with state-of-the-art methods on seven benchmark datasets, both visually and via established quantitative measurements. The results demonstrate the superiority of our method over baselines such as t-SNE and UMAP. We also provide out-of-sample extension, large-scale extension and mini-batch extension for our LaptSNE to facilitate dimensionality reduction in various scenarios.
Graph few-shot learning is of great importance among various graph learning tasks. Under the few-shot scenario, models are often required to conduct classification given limited labeled samples. Existing graph few-shot learning methods typically leverage Graph Neural Networks (GNNs) and perform classification across a series of meta-tasks. Nevertheless, these methods generally rely on the original graph (i.e., the graph that the meta-task is sampled from) to learn node representations. Consequently, the graph structure used in each meta-task is identical. Since the class sets are different across meta-tasks, node representations should be learned in a task-specific manner to promote classification performance. Therefore, to adaptively learn node representations across meta-tasks, we propose a novel framework that learns a task-specific structure for each meta-task. To handle the variety of nodes across meta-tasks, we extract relevant nodes and learn task-specific structures based on node influence and mutual information. In this way, we can learn node representations with the task-specific structure tailored for each meta-task. We further conduct extensive experiments on five node classification datasets under both single- and multiple-graph settings to validate the superiority of our framework over the state-of-the-art baselines. Our code is provided at //github.com/SongW-SW/GLITTER.
In domains where sample sizes are limited, efficient learning algorithms are critical. Learning using privileged information (LuPI) offers increased sample efficiency by allowing prediction models access to auxiliary information at training time which is unavailable when the models are used. In recent work, it was shown that for prediction in linear-Gaussian dynamical systems, a LuPI learner with access to intermediate time series data is never worse and often better in expectation than any unbiased classical learner. We provide new insights into this analysis and generalize it to nonlinear prediction tasks in latent dynamical systems, extending theoretical guarantees to the case where the map connecting latent variables and observations is known up to a linear transform. In addition, we propose algorithms based on random features and representation learning for the case when this map is unknown. A suite of empirical results confirm theoretical findings and show the potential of using privileged time-series information in nonlinear prediction.
Feature selection plays a vital role in promoting the classifier's performance. However, current methods ineffectively distinguish the complex interaction in the selected features. To further remove these hidden negative interactions, we propose a GA-like dynamic probability (GADP) method with mutual information which has a two-layer structure. The first layer applies the mutual information method to obtain a primary feature subset. The GA-like dynamic probability algorithm, as the second layer, mines more supportive features based on the former candidate features. Essentially, the GA-like method is one of the population-based algorithms so its work mechanism is similar to the GA. Different from the popular works which frequently focus on improving GA's operators for enhancing the search ability and lowering the converge time, we boldly abandon GA's operators and employ the dynamic probability that relies on the performance of each chromosome to determine feature selection in the new generation. The dynamic probability mechanism significantly reduces the parameter number in GA that making it easy to use. As each gene's probability is independent, the chromosome variety in GADP is more notable than in traditional GA, which ensures GADP has a wider search space and selects relevant features more effectively and accurately. To verify our method's superiority, we evaluate our method under multiple conditions on 15 datasets. The results demonstrate the outperformance of the proposed method. Generally, it has the best accuracy. Further, we also compare the proposed model to the popular heuristic methods like POS, FPA, and WOA. Our model still owns advantages over them.
Simulation-based Bayesian inference (SBI) can be used to estimate the parameters of complex mechanistic models given observed model outputs without requiring access to explicit likelihood evaluations. A prime example for the application of SBI in neuroscience involves estimating the parameters governing the response dynamics of Hodgkin-Huxley (HH) models from electrophysiological measurements, by inferring a posterior over the parameters that is consistent with a set of observations. To this end, many SBI methods employ a set of summary statistics or scientifically interpretable features to estimate a surrogate likelihood or posterior. However, currently, there is no way to identify how much each summary statistic or feature contributes to reducing posterior uncertainty. To address this challenge, one could simply compare the posteriors with and without a given feature included in the inference process. However, for large or nested feature sets, this would necessitate repeatedly estimating the posterior, which is computationally expensive or even prohibitive. Here, we provide a more efficient approach based on the SBI method neural likelihood estimation (NLE): We show that one can marginalize the trained surrogate likelihood post-hoc before inferring the posterior to assess the contribution of a feature. We demonstrate the usefulness of our method by identifying the most important features for inferring parameters of an example HH neuron model. Beyond neuroscience, our method is generally applicable to SBI workflows that rely on data features for inference used in other scientific fields.
Existing video denoising methods typically assume noisy videos are degraded from clean videos by adding Gaussian noise. However, deep models trained on such a degradation assumption will inevitably give rise to poor performance for real videos due to degradation mismatch. Although some studies attempt to train deep models on noisy and noise-free video pairs captured by cameras, such models can only work well for specific cameras and do not generalize well for other videos. In this paper, we propose to lift this limitation and focus on the problem of general real video denoising with the aim to generalize well on unseen real-world videos. We tackle this problem by firstly investigating the common behaviors of video noises and observing two important characteristics: 1) downscaling helps to reduce the noise level in spatial space and 2) the information from the adjacent frames help to remove the noise of current frame in temporal space. Motivated by these two observations, we propose a multi-scale recurrent architecture by making full use of the above two characteristics. Secondly, we propose a synthetic real noise degradation model by randomly shuffling different noise types to train the denoising model. With a synthesized and enriched degradation space, our degradation model can help to bridge the distribution gap between training data and real-world data. Extensive experiments demonstrate that our proposed method achieves the state-of-the-art performance and better generalization ability than existing methods on both synthetic Gaussian denoising and practical real video denoising.
Over the past few years, the rapid development of deep learning technologies for computer vision has greatly promoted the performance of medical image segmentation (MedISeg). However, the recent MedISeg publications usually focus on presentations of the major contributions (e.g., network architectures, training strategies, and loss functions) while unwittingly ignoring some marginal implementation details (also known as "tricks"), leading to a potential problem of the unfair experimental result comparisons. In this paper, we collect a series of MedISeg tricks for different model implementation phases (i.e., pre-training model, data pre-processing, data augmentation, model implementation, model inference, and result post-processing), and experimentally explore the effectiveness of these tricks on the consistent baseline models. Compared to paper-driven surveys that only blandly focus on the advantages and limitation analyses of segmentation models, our work provides a large number of solid experiments and is more technically operable. With the extensive experimental results on both the representative 2D and 3D medical image datasets, we explicitly clarify the effect of these tricks. Moreover, based on the surveyed tricks, we also open-sourced a strong MedISeg repository, where each of its components has the advantage of plug-and-play. We believe that this milestone work not only completes a comprehensive and complementary survey of the state-of-the-art MedISeg approaches, but also offers a practical guide for addressing the future medical image processing challenges including but not limited to small dataset learning, class imbalance learning, multi-modality learning, and domain adaptation. The code has been released at: //github.com/hust-linyi/MedISeg
Over the past few years, we have seen fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. At the same time, the amount of data collected in a wide array of scientific domains is dramatically increasing in both size and complexity. Taken together, this suggests many exciting opportunities for deep learning applications in scientific settings. But a significant challenge to this is simply knowing where to start. The sheer breadth and diversity of different deep learning techniques makes it difficult to determine what scientific problems might be most amenable to these methods, or which specific combination of methods might offer the most promising first approach. In this survey, we focus on addressing this central issue, providing an overview of many widely used deep learning models, spanning visual, sequential and graph structured data, associated tasks and different training methods, along with techniques to use deep learning with less data and better interpret these complex models --- two central considerations for many scientific use cases. We also include overviews of the full design process, implementation tips, and links to a plethora of tutorials, research summaries and open-sourced deep learning pipelines and pretrained models, developed by the community. We hope that this survey will help accelerate the use of deep learning across different scientific domains.
Federated learning is a new distributed machine learning framework, where a bunch of heterogeneous clients collaboratively train a model without sharing training data. In this work, we consider a practical and ubiquitous issue in federated learning: intermittent client availability, where the set of eligible clients may change during the training process. Such an intermittent client availability model would significantly deteriorate the performance of the classical Federated Averaging algorithm (FedAvg for short). We propose a simple distributed non-convex optimization algorithm, called Federated Latest Averaging (FedLaAvg for short), which leverages the latest gradients of all clients, even when the clients are not available, to jointly update the global model in each iteration. Our theoretical analysis shows that FedLaAvg attains the convergence rate of $O(1/(N^{1/4} T^{1/2}))$, achieving a sublinear speedup with respect to the total number of clients. We implement and evaluate FedLaAvg with the CIFAR-10 dataset. The evaluation results demonstrate that FedLaAvg indeed reaches a sublinear speedup and achieves 4.23% higher test accuracy than FedAvg.
With the rapid increase of large-scale, real-world datasets, it becomes critical to address the problem of long-tailed data distribution (i.e., a few classes account for most of the data, while most classes are under-represented). Existing solutions typically adopt class re-balancing strategies such as re-sampling and re-weighting based on the number of observations for each class. In this work, we argue that as the number of samples increases, the additional benefit of a newly added data point will diminish. We introduce a novel theoretical framework to measure data overlap by associating with each sample a small neighboring region rather than a single point. The effective number of samples is defined as the volume of samples and can be calculated by a simple formula $(1-\beta^{n})/(1-\beta)$, where $n$ is the number of samples and $\beta \in [0,1)$ is a hyperparameter. We design a re-weighting scheme that uses the effective number of samples for each class to re-balance the loss, thereby yielding a class-balanced loss. Comprehensive experiments are conducted on artificially induced long-tailed CIFAR datasets and large-scale datasets including ImageNet and iNaturalist. Our results show that when trained with the proposed class-balanced loss, the network is able to achieve significant performance gains on long-tailed datasets.
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