Multivariate Item Response Theory (MIRT) is sought-after widely by applied researchers looking for interpretable (sparse) explanations underlying response patterns in questionnaire data. There is, however, an unmet demand for such sparsity discovery tools in practice. Our paper develops a Bayesian platform for binary and ordinal item MIRT which requires minimal tuning and scales well on large datasets due to its parallelizable features. Bayesian methodology for MIRT models has traditionally relied on MCMC simulation, which cannot only be slow in practice, but also often renders exact sparsity recovery impossible without additional thresholding. In this work, we develop a scalable Bayesian EM algorithm to estimate sparse factor loadings from mixed continuous, binary, and ordinal item responses. We address the seemingly insurmountable problem of unknown latent factor dimensionality with tools from Bayesian nonparametrics which enable estimating the number of factors. Rotations to sparsity through parameter expansion further enhance convergence and interpretability without identifiability constraints. In our simulation study, we show that our method reliably recovers both the factor dimensionality as well as the latent structure on high-dimensional synthetic data even for small samples. We demonstrate the practical usefulness of our approach on three datasets: an educational assessment dataset, a quality-of-life measurement dataset, and a bio-behavioral dataset. All demonstrations show that our tool yields interpretable estimates, facilitating interesting discoveries that might otherwise go unnoticed under a pure confirmatory factor analysis setting.
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Functional Principal Components Analysis (FPCA) is one of the most successful and widely used analytic tools for exploration and dimension reduction of functional data. Standard implementations of FPCA estimate the principal components from the data but ignore their sampling variability in subsequent inferences. To address this problem, we propose the Fast Bayesian Functional Principal Components Analysis (Fast BayesFPCA), that treats principal components as parameters on the Stiefel manifold. To ensure efficiency, stability, and scalability we introduce three innovations: (1) project all eigenfunctions onto an orthonormal spline basis, reducing modeling considerations to a smaller-dimensional Stiefel manifold; (2) induce a uniform prior on the Stiefel manifold of the principal component spline coefficients via the polar representation of a matrix with entries following independent standard Normal priors; and (3) constrain sampling using the assumed FPCA structure to improve stability. We demonstrate the application of Fast BayesFPCA to characterize the variability in mealtime glucose from the Dietary Approaches to Stop Hypertension for Diabetes Continuous Glucose Monitoring (DASH4D CGM) study. All relevant STAN code and simulation routines are available as supplementary material.
Graph Neural Networks (GNNs) are currently one of the most powerful types of neural network architectures. Their advantage lies in the ability to leverage both the graph topology, which represents the relationships between samples, and the features of the samples themselves. However, the given graph topology often contains noisy edges, and GNNs are vulnerable to noise in the graph structure. This issue remains unresolved. In this paper, we propose using adversarial robustness evaluation to select a small subset of robust nodes that are less affected by noise. We then only feed the features of these robust nodes, along with the KNN graph constructed from these nodes, into the GNN for classification. Additionally, we compute the centroids for each class. For the remaining non-robust nodes, we assign them to the class whose centroid is closest to them. Experimental results show that this method significantly improves the accuracy of GNNs.
Large Language Models (LLMs), while being increasingly dominant on a myriad of knowledge-intensive activities, have only had limited success understanding lengthy table-text mixtures, such as academic papers and financial reports. Recent advances of long-context LLMs have opened up new possibilities for this field. Nonetheless, we identify two roadblocks: (1) Prior benchmarks of table question answering (TableQA) have focused on isolated tables without context, making it hard to evaluate models in real-world scenarios. (2) Prior benchmarks have focused on some narrow skill sets of table comprehension such as table recognition, data manipulation/calculation, table summarization etc., while a skilled human employs those skills collectively. In this work, we introduce TableQuest, a new benchmark designed to evaluate the holistic table comprehension capabilities of LLMs in the natural table-rich context of financial reports. We employ a rigorous data processing and filtering procedure to ensure that the question-answer pairs are logical, reasonable, and diverse. We experiment with 7 state-of-the-art models, and find that despite reasonable accuracy in locating facts, they often falter when required to execute more sophisticated reasoning or multi-step calculations. We conclude with a qualitative study of the failure modes and discuss the challenges of constructing a challenging benchmark. We make the evaluation data, judging procedure and results of this study publicly available to facilitate research in this field.
Gaussian Processes (GPs) are widely seen as the state-of-the-art surrogate models for Bayesian optimization (BO) due to their ability to model uncertainty and their performance on tasks where correlations are easily captured (such as those defined by Euclidean metrics) and their ability to be efficiently updated online. However, the performance of GPs depends on the choice of kernel, and kernel selection for complex correlation structures is often difficult or must be made bespoke. While Bayesian neural networks (BNNs) are a promising direction for higher capacity surrogate models, they have so far seen limited use due to poor performance on some problem types. In this paper, we propose an approach which shows competitive performance on many problem types, including some that BNNs typically struggle with. We build on variational Bayesian last layers (VBLLs), and connect training of these models to exact conditioning in GPs. We exploit this connection to develop an efficient online training algorithm that interleaves conditioning and optimization. Our findings suggest that VBLL networks significantly outperform GPs and other BNN architectures on tasks with complex input correlations, and match the performance of well-tuned GPs on established benchmark tasks.
Multimodal Knowledge Graph Construction (MMKC) refers to the process of creating a structured representation of entities and relationships through multiple modalities such as text, images, videos, etc. However, existing MMKC models have limitations in handling the introduction of new entities and relations due to the dynamic nature of the real world. Moreover, most state-of-the-art studies in MMKC only consider entity and relation extraction from text data while neglecting other multi-modal sources. Meanwhile, the current continual setting for knowledge graph construction only consider entity and relation extraction from text data while neglecting other multi-modal sources. Therefore, there arises the need to explore the challenge of continuous multimodal knowledge graph construction to address the phenomenon of catastrophic forgetting and ensure the retention of past knowledge extracted from different forms of data. This research focuses on investigating this complex topic by developing lifelong multimodal benchmark datasets. Based on the empirical findings that several state-of-the-art MMKC models, when trained on multimedia data, might unexpectedly underperform compared to those solely utilizing textual resources in a continual setting, we propose a Lifelong MultiModal Consistent Transformer Framework (LMC) for continuous multimodal knowledge graph construction. By combining the advantages of consistent KGC strategies within the context of continual learning, we achieve greater balance between stability and plasticity. Our experiments demonstrate the superior performance of our method over prevailing continual learning techniques or multimodal approaches in dynamic scenarios. Code and datasets can be found at //github.com/zjunlp/ContinueMKGC.
Graph Neural Networks (GNNs) have been successfully used in many problems involving graph-structured data, achieving state-of-the-art performance. GNNs typically employ a message-passing scheme, in which every node aggregates information from its neighbors using a permutation-invariant aggregation function. Standard well-examined choices such as the mean or sum aggregation functions have limited capabilities, as they are not able to capture interactions among neighbors. In this work, we formalize these interactions using an information-theoretic framework that notably includes synergistic information. Driven by this definition, we introduce the Graph Ordering Attention (GOAT) layer, a novel GNN component that captures interactions between nodes in a neighborhood. This is achieved by learning local node orderings via an attention mechanism and processing the ordered representations using a recurrent neural network aggregator. This design allows us to make use of a permutation-sensitive aggregator while maintaining the permutation-equivariance of the proposed GOAT layer. The GOAT model demonstrates its increased performance in modeling graph metrics that capture complex information, such as the betweenness centrality and the effective size of a node. In practical use-cases, its superior modeling capability is confirmed through its success in several real-world node classification benchmarks.
Recently, a considerable literature has grown up around the theme of Graph Convolutional Network (GCN). How to effectively leverage the rich structural information in complex graphs, such as knowledge graphs with heterogeneous types of entities and relations, is a primary open challenge in the field. Most GCN methods are either restricted to graphs with a homogeneous type of edges (e.g., citation links only), or focusing on representation learning for nodes only instead of jointly propagating and updating the embeddings of both nodes and edges for target-driven objectives. This paper addresses these limitations by proposing a novel framework, namely the Knowledge Embedding based Graph Convolutional Network (KE-GCN), which combines the power of GCNs in graph-based belief propagation and the strengths of advanced knowledge embedding (a.k.a. knowledge graph embedding) methods, and goes beyond. Our theoretical analysis shows that KE-GCN offers an elegant unification of several well-known GCN methods as specific cases, with a new perspective of graph convolution. Experimental results on benchmark datasets show the advantageous performance of KE-GCN over strong baseline methods in the tasks of knowledge graph alignment and entity classification.
Graph Convolutional Networks (GCNs) have recently become the primary choice for learning from graph-structured data, superseding hash fingerprints in representing chemical compounds. However, GCNs lack the ability to take into account the ordering of node neighbors, even when there is a geometric interpretation of the graph vertices that provides an order based on their spatial positions. To remedy this issue, we propose Geometric Graph Convolutional Network (geo-GCN) which uses spatial features to efficiently learn from graphs that can be naturally located in space. Our contribution is threefold: we propose a GCN-inspired architecture which (i) leverages node positions, (ii) is a proper generalisation of both GCNs and Convolutional Neural Networks (CNNs), (iii) benefits from augmentation which further improves the performance and assures invariance with respect to the desired properties. Empirically, geo-GCN outperforms state-of-the-art graph-based methods on image classification and chemical tasks.
Embedding models for deterministic Knowledge Graphs (KG) have been extensively studied, with the purpose of capturing latent semantic relations between entities and incorporating the structured knowledge into machine learning. However, there are many KGs that model uncertain knowledge, which typically model the inherent uncertainty of relations facts with a confidence score, and embedding such uncertain knowledge represents an unresolved challenge. The capturing of uncertain knowledge will benefit many knowledge-driven applications such as question answering and semantic search by providing more natural characterization of the knowledge. In this paper, we propose a novel uncertain KG embedding model UKGE, which aims to preserve both structural and uncertainty information of relation facts in the embedding space. Unlike previous models that characterize relation facts with binary classification techniques, UKGE learns embeddings according to the confidence scores of uncertain relation facts. To further enhance the precision of UKGE, we also introduce probabilistic soft logic to infer confidence scores for unseen relation facts during training. We propose and evaluate two variants of UKGE based on different learning objectives. Experiments are conducted on three real-world uncertain KGs via three tasks, i.e. confidence prediction, relation fact ranking, and relation fact classification. UKGE shows effectiveness in capturing uncertain knowledge by achieving promising results on these tasks, and consistently outperforms baselines on these tasks.
Graph Convolutional Networks (GCNs) and their variants have experienced significant attention and have become the de facto methods for learning graph representations. GCNs derive inspiration primarily from recent deep learning approaches, and as a result, may inherit unnecessary complexity and redundant computation. In this paper, we reduce this excess complexity through successively removing nonlinearities and collapsing weight matrices between consecutive layers. We theoretically analyze the resulting linear model and show that it corresponds to a fixed low-pass filter followed by a linear classifier. Notably, our experimental evaluation demonstrates that these simplifications do not negatively impact accuracy in many downstream applications. Moreover, the resulting model scales to larger datasets, is naturally interpretable, and yields up to two orders of magnitude speedup over FastGCN.
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