Diabetes encompasses a complex landscape of glycemic control that varies widely among individuals. However, current methods do not faithfully capture this variability at the meal level. On the one hand, expert-crafted features lack the flexibility of data-driven methods; on the other hand, learned representations tend to be uninterpretable which hampers clinical adoption. In this paper, we propose a hybrid variational autoencoder to learn interpretable representations of CGM and meal data. Our method grounds the latent space to the inputs of a mechanistic differential equation, producing embeddings that reflect physiological quantities, such as insulin sensitivity, glucose effectiveness, and basal glucose levels. Moreover, we introduce a novel method to infer the glucose appearance rate, making the mechanistic model robust to unreliable meal logs. On a dataset of CGM and self-reported meals from individuals with type-2 diabetes and pre-diabetes, our unsupervised representation discovers a separation between individuals proportional to their disease severity. Our embeddings produce clusters that are up to 4x better than naive, expert, black-box, and pure mechanistic features. Our method provides a nuanced, yet interpretable, embedding space to compare glycemic control within and across individuals, directly learnable from in-the-wild data.
Causal effect estimation from observational data is a fundamental task in empirical sciences. It becomes particularly challenging when unobserved confounders are involved in a system. This paper focuses on front-door adjustment -- a classic technique which, using observed mediators allows to identify causal effects even in the presence of unobserved confounding. While the statistical properties of the front-door estimation are quite well understood, its algorithmic aspects remained unexplored for a long time. In 2022, Jeong, Tian, and Bareinboim presented the first polynomial-time algorithm for finding sets satisfying the front-door criterion in a given directed acyclic graph (DAG), with an $O(n^3(n+m))$ run time, where $n$ denotes the number of variables and $m$ the number of edges of the causal graph. In our work, we give the first linear-time, i.e., $O(n+m)$, algorithm for this task, which thus reaches the asymptotically optimal time complexity. This result implies an $O(n(n+m))$ delay enumeration algorithm of all front-door adjustment sets, again improving previous work by a factor of $n^3$. Moreover, we provide the first linear-time algorithm for finding a minimal front-door adjustment set. We offer implementations of our algorithms in multiple programming languages to facilitate practical usage and empirically validate their feasibility, even for large graphs.
Long patch validation time is a limiting factor for automated program repair (APR). Though the duality between patch validation and mutation testing is recognized, so far there exists no study of systematically adapting mutation testing techniques to general-purpose patch validation. To address this gap, we investigate existing mutation testing techniques and identify five classes of acceleration techniques that are suitable for general-purpose patch validation. Among them, mutant schemata and mutant deduplication have not been adapted to general-purpose patch validation due to the arbitrary changes that third-party APR approaches may introduce. This presents two problems for adaption: 1) the difficulty of implementing the static equivalence analysis required by the state-of-the-art mutant deduplication approach; 2) the difficulty of capturing the changes of patches to the system state at runtime. To overcome these problems, we propose two novel approaches: 1) execution scheduling, which detects the equivalence between patches online, avoiding the static equivalence analysis and its imprecision; 2) interception-based instrumentation, which intercepts the changes of patches to the system state, avoiding a full interpreter and its overhead. Based on the contributions above, we implement ExpressAPR, a general-purpose patch validator for Java that integrates all recognized classes of techniques suitable for patch validation. Our large-scale evaluation with four APR approaches shows that ExpressAPR accelerates patch validation by 137.1x over plainvalidation or 8.8x over the state-of-the-art approach, making patch validation no longer the time bottleneck of APR. Patch validation time for a single bug can be reduced to within a few minutes on mainstream CPUs.
PageRank is a popular centrality metric that assigns importance to the vertices of a graph based on its neighbors and their score. Efficient parallel algorithms for updating PageRank on dynamic graphs is crucial for various applications, especially as dataset sizes have reached substantial scales. This technical report presents our Dynamic Frontier approach. Given a batch update of edge deletion and insertions, it progressively identifies affected vertices that are likely to change their ranks with minimal overhead. On a server equipped with a 64-core AMD EPYC-7742 processor, our Dynamic Frontier PageRank outperforms Static, Naive-dynamic, and Dynamic Traversal PageRank by 7.8x, 2.9x, and 3.9x respectively - on uniformly random batch updates of size 10^-7 |E| to 10^-3 |E|. In addition, our approach improves performance at an average rate of 1.8x for every doubling of threads.
The family of log-concave density functions contains various kinds of common probability distributions. Due to the shape restriction, it is possible to find the nonparametric estimate of the density, for example, the nonparametric maximum likelihood estimate (NPMLE). However, the associated uncertainty quantification of the NPMLE is less well developed. The current techniques for uncertainty quantification are Bayesian, using a Dirichlet process prior combined with the use of Markov chain Monte Carlo (MCMC) to sample from the posterior. In this paper, we start with the NPMLE and use a version of the martingale posterior distribution to establish uncertainty about the NPMLE. The algorithm can be implemented in parallel and hence is fast. We prove the convergence of the algorithm by constructing suitable submartingales. We also illustrate results with different models and settings and some real data, and compare our method with that within the literature.
Convolutional neural networks have shown to be widely applicable to a large number of fields when large amounts of labelled data are available. The recent trend has been to use models with increasingly larger sets of tunable parameters to increase model accuracy, reduce model loss, or create more adversarially robust models -- goals that are often at odds with one another. In particular, recent theoretical work raises questions about the ability for even larger models to generalize to data outside of the controlled train and test sets. As such, we examine the role of the number of hidden layers in the ResNet model, demonstrated on the MNIST, CIFAR10, CIFAR100 datasets. We test a variety of parameters including the size of the model, the floating point precision, and the noise level of both the training data and the model output. To encapsulate the model's predictive power and computational cost, we provide a method that uses induced failures to model the probability of failure as a function of time and relate that to a novel metric that allows us to quickly determine whether or not the cost of training a model outweighs the cost of attacking it. Using this approach, we are able to approximate the expected failure rate using a small number of specially crafted samples rather than increasingly larger benchmark datasets. We demonstrate the efficacy of this technique on both the MNIST and CIFAR10 datasets using 8-, 16-, 32-, and 64-bit floating-point numbers, various data pre-processing techniques, and several attacks on five configurations of the ResNet model. Then, using empirical measurements, we examine the various trade-offs between cost, robustness, latency, and reliability to find that larger models do not significantly aid in adversarial robustness despite costing significantly more to train.
Graph Convolutional Networks (GCNs) have been widely applied in various fields due to their significant power on processing graph-structured data. Typical GCN and its variants work under a homophily assumption (i.e., nodes with same class are prone to connect to each other), while ignoring the heterophily which exists in many real-world networks (i.e., nodes with different classes tend to form edges). Existing methods deal with heterophily by mainly aggregating higher-order neighborhoods or combing the immediate representations, which leads to noise and irrelevant information in the result. But these methods did not change the propagation mechanism which works under homophily assumption (that is a fundamental part of GCNs). This makes it difficult to distinguish the representation of nodes from different classes. To address this problem, in this paper we design a novel propagation mechanism, which can automatically change the propagation and aggregation process according to homophily or heterophily between node pairs. To adaptively learn the propagation process, we introduce two measurements of homophily degree between node pairs, which is learned based on topological and attribute information, respectively. Then we incorporate the learnable homophily degree into the graph convolution framework, which is trained in an end-to-end schema, enabling it to go beyond the assumption of homophily. More importantly, we theoretically prove that our model can constrain the similarity of representations between nodes according to their homophily degree. Experiments on seven real-world datasets demonstrate that this new approach outperforms the state-of-the-art methods under heterophily or low homophily, and gains competitive performance under homophily.
Recently, graph neural networks (GNNs) have been widely used for document classification. However, most existing methods are based on static word co-occurrence graphs without sentence-level information, which poses three challenges:(1) word ambiguity, (2) word synonymity, and (3) dynamic contextual dependency. To address these challenges, we propose a novel GNN-based sparse structure learning model for inductive document classification. Specifically, a document-level graph is initially generated by a disjoint union of sentence-level word co-occurrence graphs. Our model collects a set of trainable edges connecting disjoint words between sentences and employs structure learning to sparsely select edges with dynamic contextual dependencies. Graphs with sparse structures can jointly exploit local and global contextual information in documents through GNNs. For inductive learning, the refined document graph is further fed into a general readout function for graph-level classification and optimization in an end-to-end manner. Extensive experiments on several real-world datasets demonstrate that the proposed model outperforms most state-of-the-art results, and reveal the necessity to learn sparse structures for each document.
Most recent semantic segmentation methods adopt a fully-convolutional network (FCN) with an encoder-decoder architecture. The encoder progressively reduces the spatial resolution and learns more abstract/semantic visual concepts with larger receptive fields. Since context modeling is critical for segmentation, the latest efforts have been focused on increasing the receptive field, through either dilated/atrous convolutions or inserting attention modules. However, the encoder-decoder based FCN architecture remains unchanged. In this paper, we aim to provide an alternative perspective by treating semantic segmentation as a sequence-to-sequence prediction task. Specifically, we deploy a pure transformer (ie, without convolution and resolution reduction) to encode an image as a sequence of patches. With the global context modeled in every layer of the transformer, this encoder can be combined with a simple decoder to provide a powerful segmentation model, termed SEgmentation TRansformer (SETR). Extensive experiments show that SETR achieves new state of the art on ADE20K (50.28% mIoU), Pascal Context (55.83% mIoU) and competitive results on Cityscapes. Particularly, we achieve the first (44.42% mIoU) position in the highly competitive ADE20K test server leaderboard.
Graph Neural Networks (GNNs) have recently become increasingly popular due to their ability to learn complex systems of relations or interactions arising in a broad spectrum of problems ranging from biology and particle physics to social networks and recommendation systems. Despite the plethora of different models for deep learning on graphs, few approaches have been proposed thus far for dealing with graphs that present some sort of dynamic nature (e.g. evolving features or connectivity over time). In this paper, we present Temporal Graph Networks (TGNs), a generic, efficient framework for deep learning on dynamic graphs represented as sequences of timed events. Thanks to a novel combination of memory modules and graph-based operators, TGNs are able to significantly outperform previous approaches being at the same time more computationally efficient. We furthermore show that several previous models for learning on dynamic graphs can be cast as specific instances of our framework. We perform a detailed ablation study of different components of our framework and devise the best configuration that achieves state-of-the-art performance on several transductive and inductive prediction tasks for dynamic graphs.
Object detection typically assumes that training and test data are drawn from an identical distribution, which, however, does not always hold in practice. Such a distribution mismatch will lead to a significant performance drop. In this work, we aim to improve the cross-domain robustness of object detection. We tackle the domain shift on two levels: 1) the image-level shift, such as image style, illumination, etc, and 2) the instance-level shift, such as object appearance, size, etc. We build our approach based on the recent state-of-the-art Faster R-CNN model, and design two domain adaptation components, on image level and instance level, to reduce the domain discrepancy. The two domain adaptation components are based on H-divergence theory, and are implemented by learning a domain classifier in adversarial training manner. The domain classifiers on different levels are further reinforced with a consistency regularization to learn a domain-invariant region proposal network (RPN) in the Faster R-CNN model. We evaluate our newly proposed approach using multiple datasets including Cityscapes, KITTI, SIM10K, etc. The results demonstrate the effectiveness of our proposed approach for robust object detection in various domain shift scenarios.