arXiv subjects

Xiao Qin

Publications and source records attributed to Xiao Qin.

27 records · Page 2Linked to original sources

arXiv2024

4DBInfer: A 4D Benchmarking Toolbox for Graph-Centric Predictive Modeling on Relational DBs

Although RDBs store vast amounts of rich, informative data spread across interconnected tables, the progress of predictive machine learning models as applied to such tasks arguably falls well behind advances in other domains such as computer vision or natural language processing. This deficit stems, at least in part, from the lack of established/public RDB benchmarks as needed for training and evaluation purposes. As a result, related model development thus far often defaults to tabular approaches trained on ubiquitous single-table benchmarks, or on the relational side, graph-based alternatives such as GNNs applied to a completely different set of graph datasets devoid of tabular characteristics. To more precisely target RDBs lying at the nexus of these two complementary regimes, we explore a broad class of baseline models predicated on: (i) converting multi-table datasets into graphs using various strategies equipped with efficient subsampling, while preserving tabular characteristics; and (ii) trainable models with well-matched inductive biases that output predictions based on these input subgraphs. Then, to address the dearth of suitable public benchmarks and reduce siloed comparisons, we assemble a diverse collection of (i) large-scale RDB datasets and (ii) coincident predictive tasks. From a delivery standpoint, we operationalize the above four dimensions (4D) of exploration within a unified, scalable open-source toolbox called 4DBInfer. We conclude by presenting evaluations using 4DBInfer, the results of which highlight the importance of considering each such dimension in the design of RDB predictive models, as well as the limitations of more naive approaches such as simply joining adjacent tables. Our source code is released at https://github.com/awslabs/multi-table-benchmark .

cs.LG↗

arXiv2024

OmniMatch: Effective Self-Supervised Any-Join Discovery in Tabular Data Repositories

How can we discover join relationships among columns of tabular data in a data repository? Can this be done effectively when metadata is missing? Traditional column matching works mainly rely on similarity measures based on exact value overlaps, hence missing important semantics or failing to handle noise in the data. At the same time, recent dataset discovery methods focusing on deep table representation learning techniques, do not take into consideration the rich set of column similarity signals found in prior matching and discovery methods. Finally, existing methods heavily depend on user-provided similarity thresholds, hindering their deployability in real-world settings. In this paper, we propose OmniMatch, a novel join discovery technique that detects equi-joins and fuzzy-joins betwen columns by combining column-pair similarity measures with Graph Neural Networks (GNNs). OmniMatch's GNN can capture column relatedness leveraging graph transitivity, significantly improving the recall of join discovery tasks. At the same time, OmniMatch also increases the precision by augmenting its training data with negative column join examples through an automated negative example generation process. Most importantly, compared to the state-of-the-art matching and discovery methods, OmniMatch exhibits up to 14% higher effectiveness in F1 score and AUC without relying on metadata or user-provided thresholds for each similarity metric.

cs.DB↗

arXiv2024

Quantum fluctuations and unusual critical exponents in a quantum Rabi Triangle

Quantum fluctuations of a quantum Rabi triangle are studied using an analytical approach beyond the mean-field theory. By applying an artificial magnetic field among three cavities, time-reversal symmetry breaking is manifested through a directional transfer dynamics of photons. In contrast to previous studies, we focus on the scaling exponents of the fluctuations of the local photon number and the position variance near the critical point. By accurate calculation using Bogoliubov transformation we show that two scaling laws emerge respectively for the frustrated cavity and the remaining cavities, which are associated with the geometric frustrations. Especially, for the frustrated cavity, the scaling exponent in the chiral superradiant phase is different from that in the frustrated antiferromagnetic superradiant phase without an artificial magnetic field. The unusual scaling exponents predict distinct universality classes from the single-cavity Rabi universality. We suggest that the accurate critical exponents in few-body system is useful for identifying exotic quantum phase transition in light-matter coupling system.

quant-ph↗

arXiv2023

OrthoReg: Improving Graph-regularized MLPs via Orthogonality Regularization

Graph Neural Networks (GNNs) are currently dominating in modeling graph-structure data, while their high reliance on graph structure for inference significantly impedes them from widespread applications. By contrast, Graph-regularized MLPs (GR-MLPs) implicitly inject the graph structure information into model weights, while their performance can hardly match that of GNNs in most tasks. This motivates us to study the causes of the limited performance of GR-MLPs. In this paper, we first demonstrate that node embeddings learned from conventional GR-MLPs suffer from dimensional collapse, a phenomenon in which the largest a few eigenvalues dominate the embedding space, through empirical observations and theoretical analysis. As a result, the expressive power of the learned node representations is constrained. We further propose OrthoReg, a novel GR-MLP model to mitigate the dimensional collapse issue. Through a soft regularization loss on the correlation matrix of node embeddings, OrthoReg explicitly encourages orthogonal node representations and thus can naturally avoid dimensionally collapsed representations. Experiments on traditional transductive semi-supervised classification tasks and inductive node classification for cold-start scenarios demonstrate its effectiveness and superiority.

cs.LG↗

arXiv2022

Detecting Temporal shape changes with the Euler Characteristic Transform

Organoids are multi-cellular structures which are cultured in vitro from stem cells to resemble specific organs (e.g., brain, liver) in their three-dimensional composition. Dynamic changes in the shape and composition of these model systems can be used to understand the effect of mutations and treatments in health and disease. In this paper, we propose a new technique in the field of topological data analysis for DEtecting Temporal shape changes with the Euler Characteristic Transform (DETECT). DETECT is a rotationally invariant signature of dynamically changing shapes. We demonstrate our method on a data set of segmented videos of mouse small intestine organoid experiments and show that it outperforms classical shape descriptors. We verify our method on a synthetic organoid data set and illustrate how it generalises to 3D. We conclude that DETECT offers rigorous quantification of organoids and opens up computationally scalable methods for distinguishing different growth regimes and assessing treatment effects.

q-bio.QM↗

arXiv2022

Scaling Knowledge Graph Embedding Models

Developing scalable solutions for training Graph Neural Networks (GNNs) for link prediction tasks is challenging due to the high data dependencies which entail high computational cost and huge memory footprint. We propose a new method for scaling training of knowledge graph embedding models for link prediction to address these challenges. Towards this end, we propose the following algorithmic strategies: self-sufficient partitions, constraint-based negative sampling, and edge mini-batch training. Both, partitioning strategy and constraint-based negative sampling, avoid cross partition data transfer during training. In our experimental evaluation, we show that our scaling solution for GNN-based knowledge graph embedding models achieves a 16x speed up on benchmark datasets while maintaining a comparable model performance as non-distributed methods on standard metrics.

cs.LG↗

arXiv2021

Medical Entity Disambiguation Using Graph Neural Networks

Medical knowledge bases (KBs), distilled from biomedical literature and regulatory actions, are expected to provide high-quality information to facilitate clinical decision making. Entity disambiguation (also referred to as entity linking) is considered as an essential task in unlocking the wealth of such medical KBs. However, existing medical entity disambiguation methods are not adequate due to word discrepancies between the entities in the KB and the text snippets in the source documents. Recently, graph neural networks (GNNs) have proven to be very effective and provide state-of-the-art results for many real-world applications with graph-structured data. In this paper, we introduce ED-GNN based on three representative GNNs (GraphSAGE, R-GCN, and MAGNN) for medical entity disambiguation. We develop two optimization techniques to fine-tune and improve ED-GNN. First, we introduce a novel strategy to represent entities that are mentioned in text snippets as a query graph. Second, we design an effective negative sampling strategy that identifies hard negative samples to improve the model's disambiguation capability. Compared to the best performing state-of-the-art solutions, our ED-GNN offers an average improvement of 7.3% in terms of F1 score on five real-world datasets.

cs.IR↗

arXiv2021

Relation-aware Graph Attention Model With Adaptive Self-adversarial Training

This paper describes an end-to-end solution for the relationship prediction task in heterogeneous, multi-relational graphs. We particularly address two building blocks in the pipeline, namely heterogeneous graph representation learning and negative sampling. Existing message passing-based graph neural networks use edges either for graph traversal and/or selection of message encoding functions. Ignoring the edge semantics could have severe repercussions on the quality of embeddings, especially when dealing with two nodes having multiple relations. Furthermore, the expressivity of the learned representation depends on the quality of negative samples used during training. Although existing hard negative sampling techniques can identify challenging negative relationships for optimization, new techniques are required to control false negatives during training as false negatives could corrupt the learning process. To address these issues, first, we propose RelGNN -- a message passing-based heterogeneous graph attention model. In particular, RelGNN generates the states of different relations and leverages them along with the node states to weigh the messages. RelGNN also adopts a self-attention mechanism to balance the importance of attribute features and topological features for generating the final entity embeddings. Second, we introduce a parameter-free negative sampling technique -- adaptive self-adversarial (ASA) negative sampling. ASA reduces the false-negative rate by leveraging positive relationships to effectively guide the identification of true negative samples. Our experimental evaluation demonstrates that RelGNN optimized by ASA for relationship prediction improves state-of-the-art performance across established benchmarks as well as on a real industrial dataset.

cs.LG↗

arXiv2021

Knowledge Graph Embedding using Graph Convolutional Networks with Relation-Aware Attention

Knowledge graph embedding methods learn embeddings of entities and relations in a low dimensional space which can be used for various downstream machine learning tasks such as link prediction and entity matching. Various graph convolutional network methods have been proposed which use different types of information to learn the features of entities and relations. However, these methods assign the same weight (importance) to the neighbors when aggregating the information, ignoring the role of different relations with the neighboring entities. To this end, we propose a relation-aware graph attention model that leverages relation information to compute different weights to the neighboring nodes for learning embeddings of entities and relations. We evaluate our proposed approach on link prediction and entity matching tasks. Our experimental results on link prediction on three datasets (one proprietary and two public) and results on unsupervised entity matching on one proprietary dataset demonstrate the effectiveness of the relation-aware attention.

cs.LG↗