Modern biomedical image analysis using deep learning often encounters the challenge of limited annotated data. To overcome this issue, deep generative models can be employed to synthesize realistic biomedical images. In this regard, we propose an image synthesis method that utilizes denoising diffusion probabilistic models (DDPMs) to automatically generate retinal optical coherence tomography (OCT) images. By providing rough layer sketches, the trained DDPMs can generate realistic circumpapillary OCT images. We further find that more accurate pseudo labels can be obtained through knowledge adaptation, which greatly benefits the segmentation task. Through this, we observe a consistent improvement in layer segmentation accuracy, which is validated using various neural networks. Furthermore, we have discovered that a layer segmentation model trained solely with synthesized images can achieve comparable results to a model trained exclusively with real images. These findings demonstrate the promising potential of DDPMs in reducing the need for manual annotations of retinal OCT images.
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Graph outlier detection is a prominent task of research and application in the realm of graph neural networks. It identifies the outlier nodes that exhibit deviation from the majority in the graph. One of the fundamental challenges confronting supervised graph outlier detection algorithms is the prevalent issue of class imbalance, where the scarcity of outlier instances compared to normal instances often results in suboptimal performance. Conventional methods mitigate the imbalance by reweighting instances in the estimation of the loss function, assigning higher weights to outliers and lower weights to inliers. Nonetheless, these strategies are prone to overfitting and underfitting, respectively. Recently, generative models, especially diffusion models, have demonstrated their efficacy in synthesizing high-fidelity images. Despite their extraordinary generation quality, their potential in data augmentation for supervised graph outlier detection remains largely underexplored. To bridge this gap, we introduce GODM, a novel data augmentation for mitigating class imbalance in supervised Graph Outlier detection with latent Diffusion Models. Specifically, our proposed method consists of three key components: (1) Variantioanl Encoder maps the heterogeneous information inherent within the graph data into a unified latent space. (2) Graph Generator synthesizes graph data that are statistically similar to real outliers from latent space, and (3) Latent Diffusion Model learns the latent space distribution of real organic data by iterative denoising. Extensive experiments conducted on multiple datasets substantiate the effectiveness and efficiency of GODM. The case study further demonstrated the generation quality of our synthetic data. To foster accessibility and reproducibility, we encapsulate GODM into a plug-and-play package and release it at the Python Package Index (PyPI).
The structure of Markov equivalence classes (MECs) of causal DAGs has been studied extensively. A natural question in this regard is to algorithmically find the number of MECs with a given skeleton. Until recently, the known results for this problem were in the setting of very special graphs (such as paths, cycles, and star graphs). More recently, a fixed-parameter tractable (FPT) algorithm was given for this problem which, given an input graph $G$, counts the number of MECs with the skeleton $G$ in $O(n(2^{O(d^4k^4)} + n^2))$ time, where $n$, $d$, and $k$, respectively, are the numbers of nodes, the degree, and the treewidth of $G$. We give a faster FPT algorithm that solves the problem in $O(n(2^{O(d^2k^2)} + n^2))$ time when the input graph is chordal. Additionally, we show that the runtime can be further improved to polynomial time when the input graph $G$ is a tree.
Neural graphics primitives are faster and achieve higher quality when their neural networks are augmented by spatial data structures that hold trainable features arranged in a grid. However, existing feature grids either come with a large memory footprint (dense or factorized grids, trees, and hash tables) or slow performance (index learning and vector quantization). In this paper, we show that a hash table with learned probes has neither disadvantage, resulting in a favorable combination of size and speed. Inference is faster than unprobed hash tables at equal quality while training is only 1.2-2.6x slower, significantly outperforming prior index learning approaches. We arrive at this formulation by casting all feature grids into a common framework: they each correspond to a lookup function that indexes into a table of feature vectors. In this framework, the lookup functions of existing data structures can be combined by simple arithmetic combinations of their indices, resulting in Pareto optimal compression and speed.
Graph Neural Networks (GNNs) have received considerable attention on graph-structured data learning for a wide variety of tasks. The well-designed propagation mechanism which has been demonstrated effective is the most fundamental part of GNNs. Although most of GNNs basically follow a message passing manner, litter effort has been made to discover and analyze their essential relations. In this paper, we establish a surprising connection between different propagation mechanisms with a unified optimization problem, showing that despite the proliferation of various GNNs, in fact, their proposed propagation mechanisms are the optimal solution optimizing a feature fitting function over a wide class of graph kernels with a graph regularization term. Our proposed unified optimization framework, summarizing the commonalities between several of the most representative GNNs, not only provides a macroscopic view on surveying the relations between different GNNs, but also further opens up new opportunities for flexibly designing new GNNs. With the proposed framework, we discover that existing works usually utilize naive graph convolutional kernels for feature fitting function, and we further develop two novel objective functions considering adjustable graph kernels showing low-pass or high-pass filtering capabilities respectively. Moreover, we provide the convergence proofs and expressive power comparisons for the proposed models. Extensive experiments on benchmark datasets clearly show that the proposed GNNs not only outperform the state-of-the-art methods but also have good ability to alleviate over-smoothing, and further verify the feasibility for designing GNNs with our unified optimization framework.
Spectral clustering (SC) is a popular clustering technique to find strongly connected communities on a graph. SC can be used in Graph Neural Networks (GNNs) to implement pooling operations that aggregate nodes belonging to the same cluster. However, the eigendecomposition of the Laplacian is expensive and, since clustering results are graph-specific, pooling methods based on SC must perform a new optimization for each new sample. In this paper, we propose a graph clustering approach that addresses these limitations of SC. We formulate a continuous relaxation of the normalized minCUT problem and train a GNN to compute cluster assignments that minimize this objective. Our GNN-based implementation is differentiable, does not require to compute the spectral decomposition, and learns a clustering function that can be quickly evaluated on out-of-sample graphs. From the proposed clustering method, we design a graph pooling operator that overcomes some important limitations of state-of-the-art graph pooling techniques and achieves the best performance in several supervised and unsupervised tasks.
Translational distance-based knowledge graph embedding has shown progressive improvements on the link prediction task, from TransE to the latest state-of-the-art RotatE. However, N-1, 1-N and N-N predictions still remain challenging. In this work, we propose a novel translational distance-based approach for knowledge graph link prediction. The proposed method includes two-folds, first we extend the RotatE from 2D complex domain to high dimension space with orthogonal transforms to model relations for better modeling capacity. Second, the graph context is explicitly modeled via two directed context representations. These context representations are used as part of the distance scoring function to measure the plausibility of the triples during training and inference. The proposed approach effectively improves prediction accuracy on the difficult N-1, 1-N and N-N cases for knowledge graph link prediction task. The experimental results show that it achieves better performance on two benchmark data sets compared to the baseline RotatE, especially on data set (FB15k-237) with many high in-degree connection nodes.
Incorporating knowledge graph into recommender systems has attracted increasing attention in recent years. By exploring the interlinks within a knowledge graph, the connectivity between users and items can be discovered as paths, which provide rich and complementary information to user-item interactions. Such connectivity not only reveals the semantics of entities and relations, but also helps to comprehend a user's interest. However, existing efforts have not fully explored this connectivity to infer user preferences, especially in terms of modeling the sequential dependencies within and holistic semantics of a path. In this paper, we contribute a new model named Knowledge-aware Path Recurrent Network (KPRN) to exploit knowledge graph for recommendation. KPRN can generate path representations by composing the semantics of both entities and relations. By leveraging the sequential dependencies within a path, we allow effective reasoning on paths to infer the underlying rationale of a user-item interaction. Furthermore, we design a new weighted pooling operation to discriminate the strengths of different paths in connecting a user with an item, endowing our model with a certain level of explainability. We conduct extensive experiments on two datasets about movie and music, demonstrating significant improvements over state-of-the-art solutions Collaborative Knowledge Base Embedding and Neural Factorization Machine.
Recently, graph neural networks (GNNs) have revolutionized the field of graph representation learning through effectively learned node embeddings, and achieved state-of-the-art results in tasks such as node classification and link prediction. However, current GNN methods are inherently flat and do not learn hierarchical representations of graphs---a limitation that is especially problematic for the task of graph classification, where the goal is to predict the label associated with an entire graph. Here we propose DiffPool, a differentiable graph pooling module that can generate hierarchical representations of graphs and can be combined with various graph neural network architectures in an end-to-end fashion. DiffPool learns a differentiable soft cluster assignment for nodes at each layer of a deep GNN, mapping nodes to a set of clusters, which then form the coarsened input for the next GNN layer. Our experimental results show that combining existing GNN methods with DiffPool yields an average improvement of 5-10% accuracy on graph classification benchmarks, compared to all existing pooling approaches, achieving a new state-of-the-art on four out of five benchmark data sets.
Visual Question Answering (VQA) models have struggled with counting objects in natural images so far. We identify a fundamental problem due to soft attention in these models as a cause. To circumvent this problem, we propose a neural network component that allows robust counting from object proposals. Experiments on a toy task show the effectiveness of this component and we obtain state-of-the-art accuracy on the number category of the VQA v2 dataset without negatively affecting other categories, even outperforming ensemble models with our single model. On a difficult balanced pair metric, the component gives a substantial improvement in counting over a strong baseline by 6.6%.
Recently, deep learning has achieved very promising results in visual object tracking. Deep neural networks in existing tracking methods require a lot of training data to learn a large number of parameters. However, training data is not sufficient for visual object tracking as annotations of a target object are only available in the first frame of a test sequence. In this paper, we propose to learn hierarchical features for visual object tracking by using tree structure based Recursive Neural Networks (RNN), which have fewer parameters than other deep neural networks, e.g. Convolutional Neural Networks (CNN). First, we learn RNN parameters to discriminate between the target object and background in the first frame of a test sequence. Tree structure over local patches of an exemplar region is randomly generated by using a bottom-up greedy search strategy. Given the learned RNN parameters, we create two dictionaries regarding target regions and corresponding local patches based on the learned hierarchical features from both top and leaf nodes of multiple random trees. In each of the subsequent frames, we conduct sparse dictionary coding on all candidates to select the best candidate as the new target location. In addition, we online update two dictionaries to handle appearance changes of target objects. Experimental results demonstrate that our feature learning algorithm can significantly improve tracking performance on benchmark datasets.
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