Learning a categorical distribution comes with its own set of challenges. A successful approach taken by state-of-the-art works is to cast the problem in a continuous domain to take advantage of the impressive performance of the generative models for continuous data. Amongst them are the recently emerging diffusion probabilistic models, which have the observed advantage of generating high-quality samples. Recent advances for categorical generative models have focused on log likelihood improvements. In this work, we propose a generative model for categorical data based on diffusion models with a focus on high-quality sample generation, and propose sampled-based evaluation methods. The efficacy of our method stems from performing diffusion in the continuous domain while having its parameterization informed by the structure of the categorical nature of the target distribution. Our method of evaluation highlights the capabilities and limitations of different generative models for generating categorical data, and includes experiments on synthetic and real-world protein datasets.
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Uncertainty quantification in medical images has become an essential addition to segmentation models for practical application in the real world. Although there are valuable developments in accurate uncertainty quantification methods using 2D images and slices of 3D volumes, in clinical practice, the complete 3D volumes (such as CT and MRI scans) are used to evaluate and plan the medical procedure. As a result, the existing 2D methods miss the rich 3D spatial information when resolving the uncertainty. A popular approach for quantifying the ambiguity in the data is to learn a distribution over the possible hypotheses. In recent work, this ambiguity has been modeled to be strictly Gaussian. Normalizing Flows (NFs) are capable of modelling more complex distributions and thus, better fit the embedding space of the data. To this end, we have developed a 3D probabilistic segmentation framework augmented with NFs, to enable capturing the distributions of various complexity. To test the proposed approach, we evaluate the model on the LIDC-IDRI dataset for lung nodule segmentation and quantify the aleatoric uncertainty introduced by the multi-annotator setting and inherent ambiguity in the CT data. Following this approach, we are the first to present a 3D Squared Generalized Energy Distance (GED) of 0.401 and a high 0.468 Hungarian-matched 3D IoU. The obtained results reveal the value in capturing the 3D uncertainty, using a flexible posterior distribution augmented with a Normalizing Flow. Finally, we present the aleatoric uncertainty in a visual manner with the aim to provide clinicians with additional insight into data ambiguity and facilitating more informed decision-making.
We propose a Bayesian approach to estimate finite population means for small areas. The proposed methodology improves on the traditional sample survey methods because, unlike the traditional methods, our proposed method borrows strength from multiple data sources. Our approach is fundamentally different from the existing small area Bayesian approach to the finite population sampling, which typically assumes a hierarchical model for all units of the finite population. We assume such model only for the units of the finite population in which the outcome variable is observed; because for these units, the assumed model can be checked using existing statistical tools. Modeling unobserved units of the finite population is challenging because the assumed model cannot be checked in the absence of data on the outcome variable. To make reasonable modeling assumptions, we propose to form several cells for each small area using factors that potentially influence the outcome variable of interest. This strategy is expected to bring some degree of homogeneity within a given cell and also among cells from different small areas that are constructed with the same factor level combination. Instead of modeling true probabilities for unobserved individual units, we assume that population means of cells with the same combination of factor levels are identical across small areas and the population mean of true probabilities for a cell is identical to the mean of true values for the observed units in that cell. We apply our proposed methodology to a real-life COVID-19 survey, linking information from multiple disparate data sources to estimate vaccine-hesitancy rates (proportions) for 50 US states and Washington, D.C. (small areas). We also provide practical ways of model selection that can be applied to a wider class of models under similar setting but for a diverse range of scientific problems.
Integer linear programming models a wide range of practical combinatorial optimization problems and has significant impacts in industry and management sectors. This work develops the first standalone local search solver for general integer linear programming validated on a large heterogeneous problem dataset. We propose a local search framework that switches in three modes, namely Search, Improve, and Restore modes, and design tailored operators adapted to different modes, thus improve the quality of the current solution according to different situations. For the Search and Restore modes, we propose an operator named tight move, which adaptively modifies variables' values trying to make some constraint tight. For the Improve mode, an efficient operator lift move is proposed to improve the quality of the objective function while maintaining feasibility. Putting these together, we develop a local search solver for integer linear programming called Local-ILP. Experiments conducted on the MIPLIB dataset show the effectiveness of our solver in solving large-scale hard integer linear programming problems within a reasonably short time. Local-ILP is competitive and complementary to the state-of-the-art commercial solver Gurobi and significantly outperforms the state-of-the-art non-commercial solver SCIP. Moreover, our solver establishes new records for 6 MIPLIB open instances.
Recent advancements in the field of natural language generation have facilitated the use of large language models to assess the quality of generated text. Although these models have shown promising results in tasks such as machine translation and summarization, their applicability in code generation tasks remains limited without human involvement. The complexity of programming concepts required for such tasks makes it difficult to develop evaluation metrics that align with human judgment. Token-matching-based metrics, such as BLEU, have demonstrated weak correlations with human practitioners in code generation tasks. Moreover, the utilization of human-written test suites to evaluate functional correctness can be challenging in domains with low resources. To overcome these obstacles, we propose a new evaluation framework based on the GPT-3.5 (\texttt{GPT-3.5-turbo}), for code generation assessments. Our framework addresses the limitations of existing approaches by achieving superior correlations with functional correctness and human preferences, without the need for test oracles or references. We evaluate the efficacy of our framework on two different tasks and four programming languages, comparing its performance with the state-of-the-art CodeBERTScore metric, which relies on a pre-trained model. Our results demonstrate that our framework surpasses CodeBERTScore, delivering high levels of accuracy and consistency across various programming languages and tasks. We also make our evaluation framework and datasets available to the public at \url{//github.com/terryyz/llm-code-eval}, encouraging further research in the evaluation of code generation.
Graphs are important data representations for describing objects and their relationships, which appear in a wide diversity of real-world scenarios. As one of a critical problem in this area, graph generation considers learning the distributions of given graphs and generating more novel graphs. Owing to their wide range of applications, generative models for graphs, which have a rich history, however, are traditionally hand-crafted and only capable of modeling a few statistical properties of graphs. Recent advances in deep generative models for graph generation is an important step towards improving the fidelity of generated graphs and paves the way for new kinds of applications. This article provides an extensive overview of the literature in the field of deep generative models for graph generation. Firstly, the formal definition of deep generative models for the graph generation and the preliminary knowledge are provided. Secondly, taxonomies of deep generative models for both unconditional and conditional graph generation are proposed respectively; the existing works of each are compared and analyzed. After that, an overview of the evaluation metrics in this specific domain is provided. Finally, the applications that deep graph generation enables are summarized and five promising future research directions are highlighted.
Designing and generating new data under targeted properties has been attracting various critical applications such as molecule design, image editing and speech synthesis. Traditional hand-crafted approaches heavily rely on expertise experience and intensive human efforts, yet still suffer from the insufficiency of scientific knowledge and low throughput to support effective and efficient data generation. Recently, the advancement of deep learning induces expressive methods that can learn the underlying representation and properties of data. Such capability provides new opportunities in figuring out the mutual relationship between the structural patterns and functional properties of the data and leveraging such relationship to generate structural data given the desired properties. This article provides a systematic review of this promising research area, commonly known as controllable deep data generation. Firstly, the potential challenges are raised and preliminaries are provided. Then the controllable deep data generation is formally defined, a taxonomy on various techniques is proposed and the evaluation metrics in this specific domain are summarized. After that, exciting applications of controllable deep data generation are introduced and existing works are experimentally analyzed and compared. Finally, the promising future directions of controllable deep data generation are highlighted and five potential challenges are identified.
Unsupervised domain adaptation has recently emerged as an effective paradigm for generalizing deep neural networks to new target domains. However, there is still enormous potential to be tapped to reach the fully supervised performance. In this paper, we present a novel active learning strategy to assist knowledge transfer in the target domain, dubbed active domain adaptation. We start from an observation that energy-based models exhibit free energy biases when training (source) and test (target) data come from different distributions. Inspired by this inherent mechanism, we empirically reveal that a simple yet efficient energy-based sampling strategy sheds light on selecting the most valuable target samples than existing approaches requiring particular architectures or computation of the distances. Our algorithm, Energy-based Active Domain Adaptation (EADA), queries groups of targe data that incorporate both domain characteristic and instance uncertainty into every selection round. Meanwhile, by aligning the free energy of target data compact around the source domain via a regularization term, domain gap can be implicitly diminished. Through extensive experiments, we show that EADA surpasses state-of-the-art methods on well-known challenging benchmarks with substantial improvements, making it a useful option in the open world. Code is available at //github.com/BIT-DA/EADA.
Evaluating the quality of learned representations without relying on a downstream task remains one of the challenges in representation learning. In this work, we present Geometric Component Analysis (GeomCA) algorithm that evaluates representation spaces based on their geometric and topological properties. GeomCA can be applied to representations of any dimension, independently of the model that generated them. We demonstrate its applicability by analyzing representations obtained from a variety of scenarios, such as contrastive learning models, generative models and supervised learning models.
Data augmentation has been widely used to improve generalizability of machine learning models. However, comparatively little work studies data augmentation for graphs. This is largely due to the complex, non-Euclidean structure of graphs, which limits possible manipulation operations. Augmentation operations commonly used in vision and language have no analogs for graphs. Our work studies graph data augmentation for graph neural networks (GNNs) in the context of improving semi-supervised node-classification. We discuss practical and theoretical motivations, considerations and strategies for graph data augmentation. Our work shows that neural edge predictors can effectively encode class-homophilic structure to promote intra-class edges and demote inter-class edges in given graph structure, and our main contribution introduces the GAug graph data augmentation framework, which leverages these insights to improve performance in GNN-based node classification via edge prediction. Extensive experiments on multiple benchmarks show that augmentation via GAug improves performance across GNN architectures and datasets.
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.
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