arXiv subjects

Yongqi Zhang

Publications and source records attributed to Yongqi Zhang.

At least 55 records · Page 3Linked to original sources

arXiv2025

Less is More: One-shot Subgraph Reasoning on Large-scale Knowledge Graphs

To deduce new facts on a knowledge graph (KG), a link predictor learns from the graph structure and collects local evidence to find the answer to a given query. However, existing methods suffer from a severe scalability problem due to the utilization of the whole KG for prediction, which hinders their promise on large scale KGs and cannot be directly addressed by vanilla sampling methods. In this work, we propose the one-shot-subgraph link prediction to achieve efficient and adaptive prediction. The design principle is that, instead of directly acting on the whole KG, the prediction procedure is decoupled into two steps, i.e., (i) extracting only one subgraph according to the query and (ii) predicting on this single, query dependent subgraph. We reveal that the non-parametric and computation-efficient heuristics Personalized PageRank (PPR) can effectively identify the potential answers and supporting evidence. With efficient subgraph-based prediction, we further introduce the automated searching of the optimal configurations in both data and model spaces. Empirically, we achieve promoted efficiency and leading performances on five large-scale benchmarks. The code is publicly available at: https://github.com/tmlr-group/one-shot-subgraph.

cs.LG↗

arXiv2024

Beyond Scaleup: Knowledge-aware Parsimony Learning from Deep Networks

The brute-force scaleup of training datasets, learnable parameters and computation power, has become a prevalent strategy for developing more robust learning models. However, due to bottlenecks in data, computation, and trust, the sustainability of this strategy is a serious concern. In this paper, we attempt to address this issue in a parsimonious manner (i.e., achieving greater potential with simpler models). The key is to drive models using domain-specific knowledge, such as symbols, logic, and formulas, instead of purely relying on scaleup. This approach allows us to build a framework that uses this knowledge as "building blocks" to achieve parsimony in model design, training, and interpretation. Empirical results show that our methods surpass those that typically follow the scaling law. We also demonstrate our framework in AI for science, specifically in the problem of drug-drug interaction prediction. We hope our research can foster more diverse technical roadmaps in the era of foundation models.

cs.LG↗

arXiv2024

R^2AG: Incorporating Retrieval Information into Retrieval Augmented Generation

Retrieval augmented generation (RAG) has been applied in many scenarios to augment large language models (LLMs) with external documents provided by retrievers. However, a semantic gap exists between LLMs and retrievers due to differences in their training objectives and architectures. This misalignment forces LLMs to passively accept the documents provided by the retrievers, leading to incomprehension in the generation process, where the LLMs are burdened with the task of distinguishing these documents using their inherent knowledge. This paper proposes R$^2$AG, a novel enhanced RAG framework to fill this gap by incorporating Retrieval information into Retrieval Augmented Generation. Specifically, R$^2$AG utilizes the nuanced features from the retrievers and employs a R$^2$-Former to capture retrieval information. Then, a retrieval-aware prompting strategy is designed to integrate retrieval information into LLMs' generation. Notably, R$^2$AG suits low-source scenarios where LLMs and retrievers are frozen. Extensive experiments across five datasets validate the effectiveness, robustness, and efficiency of R$^2$AG. Our analysis reveals that retrieval information serves as an anchor to aid LLMs in the generation process, thereby filling the semantic gap.

cs.CL↗

arXiv2024

Understanding Expressivity of GNN in Rule Learning

Rule learning is critical to improving knowledge graph (KG) reasoning due to their ability to provide logical and interpretable explanations. Recently, Graph Neural Networks (GNNs) with tail entity scoring achieve the state-of-the-art performance on KG reasoning. However, the theoretical understandings for these GNNs are either lacking or focusing on single-relational graphs, leaving what the kind of rules these GNNs can learn an open problem. We propose to fill the above gap in this paper. Specifically, GNNs with tail entity scoring are unified into a common framework. Then, we analyze their expressivity by formally describing the rule structures they can learn and theoretically demonstrating their superiority. These results further inspire us to propose a novel labeling strategy to learn more rules in KG reasoning. Experimental results are consistent with our theoretical findings and verify the effectiveness of our proposed method. The code is publicly available at https://github.com/LARS-research/Rule-learning-expressivity.

cs.LG↗

arXiv2024

BP4ER: Bootstrap Prompting for Explicit Reasoning in Medical Dialogue Generation

Medical dialogue generation (MDG) has gained increasing attention due to its substantial practical value. Previous works typically employ a sequence-to-sequence framework to generate medical responses by modeling dialogue context as sequential text with annotated medical entities. While these methods have been successful in generating fluent responses, they fail to provide process explanations of reasoning and require extensive entity annotation. To address these limitations, we propose the method Bootstrap Prompting for Explicit Reasoning in MDG (BP4ER), which explicitly model MDG's multi-step reasoning process and iteratively enhance this reasoning process. We employ a least-to-most prompting strategy to guide a large language model (LLM) in explicit reasoning, breaking down MDG into simpler sub-questions. These sub-questions build on answers from previous ones. Additionally, we also introduce two distinct bootstrapping techniques for prompting, which autonomously correct errors and facilitate the LLM's explicit reasoning. This approach eliminates the need for entity annotation and increases the transparency of the MDG process by explicitly generating the intermediate reasoning chain. The experimental findings on the two public datasets indicate that BP4ER outperforms state-of-the-art methods in terms of both objective and subjective evaluation metrics.

cs.CL↗

arXiv2024

Knowledge-Enhanced Recommendation with User-Centric Subgraph Network

Recommendation systems, as widely implemented nowadays on various platforms, recommend relevant items to users based on their preferences. The classical methods which rely on user-item interaction matrices has limitations, especially in scenarios where there is a lack of interaction data for new items. Knowledge graph (KG)-based recommendation systems have emerged as a promising solution. However, most KG-based methods adopt node embeddings, which do not provide personalized recommendations for different users and cannot generalize well to the new items. To address these limitations, we propose Knowledge-enhanced User-Centric subgraph Network (KUCNet), a subgraph learning approach with graph neural network (GNN) for effective recommendation. KUCNet constructs a U-I subgraph for each user-item pair that captures both the historical information of user-item interactions and the side information provided in KG. An attention-based GNN is designed to encode the U-I subgraphs for recommendation. Considering efficiency, the pruned user-centric computation graph is further introduced such that multiple U-I subgraphs can be simultaneously computed and that the size can be pruned by Personalized PageRank. Our proposed method achieves accurate, efficient, and interpretable recommendations especially for new items. Experimental results demonstrate the superiority of KUCNet over state-of-the-art KG-based and collaborative filtering (CF)-based methods.

cs.IR↗

arXiv2024

Learning to Describe for Predicting Zero-shot Drug-Drug Interactions

Adverse drug-drug interactions~(DDIs) can compromise the effectiveness of concurrent drug administration, posing a significant challenge in healthcare. As the development of new drugs continues, the potential for unknown adverse effects resulting from DDIs becomes a growing concern. Traditional computational methods for DDI prediction may fail to capture interactions for new drugs due to the lack of knowledge. In this paper, we introduce a new problem setup as zero-shot DDI prediction that deals with the case of new drugs. Leveraging textual information from online databases like DrugBank and PubChem, we propose an innovative approach TextDDI with a language model-based DDI predictor and a reinforcement learning~(RL)-based information selector, enabling the selection of concise and pertinent text for accurate DDI prediction on new drugs. Empirical results show the benefits of the proposed approach on several settings including zero-shot and few-shot DDI prediction, and the selected texts are semantically relevant. Our code and data are available at \url{https://github.com/zhufq00/DDIs-Prediction}.

cs.CL↗

arXiv2024

Automated Machine Learning: From Principles to Practices

Machine learning (ML) methods have been developing rapidly, but configuring and selecting proper methods to achieve a desired performance is increasingly difficult and tedious. To address this challenge, automated machine learning (AutoML) has emerged, which aims to generate satisfactory ML configurations for given tasks in a data-driven way. In this paper, we provide a comprehensive survey on this topic. We begin with the formal definition of AutoML and then introduce its principles, including the bi-level learning objective, the learning strategy, and the theoretical interpretation. Then, we summarize the AutoML practices by setting up the taxonomy of existing works based on three main factors: the search space, the search algorithm, and the evaluation strategy. Each category is also explained with the representative methods. Then, we illustrate the principles and practices with exemplary applications from configuring ML pipeline, one-shot neural architecture search, and integration with foundation models. Finally, we highlight the emerging directions of AutoML and conclude the survey.

cs.AI↗

arXiv2023

Emerging Drug Interaction Prediction Enabled by Flow-based Graph Neural Network with Biomedical Network

Accurately predicting drug-drug interactions (DDI) for emerging drugs, which offer possibilities for treating and alleviating diseases, with computational methods can improve patient care and contribute to efficient drug development. However, many existing computational methods require large amounts of known DDI information, which is scarce for emerging drugs. In this paper, we propose EmerGNN, a graph neural network (GNN) that can effectively predict interactions for emerging drugs by leveraging the rich information in biomedical networks. EmerGNN learns pairwise representations of drugs by extracting the paths between drug pairs, propagating information from one drug to the other, and incorporating the relevant biomedical concepts on the paths. The different edges on the biomedical network are weighted to indicate the relevance for the target DDI prediction. Overall, EmerGNN has higher accuracy than existing approaches in predicting interactions for emerging drugs and can identify the most relevant information on the biomedical network.

q-bio.QM↗

arXiv2023

Positive-Unlabeled Node Classification with Structure-aware Graph Learning

Node classification on graphs is an important research problem with many applications. Real-world graph data sets may not be balanced and accurate as assumed by most existing works. A challenging setting is positive-unlabeled (PU) node classification, where labeled nodes are restricted to positive nodes. It has diverse applications, e.g., pandemic prediction or network anomaly detection. Existing works on PU node classification overlook information in the graph structure, which can be critical. In this paper, we propose to better utilize graph structure for PU node classification. We first propose a distance-aware PU loss that uses homophily in graphs to introduce more accurate supervision. We also propose a regularizer to align the model with graph structure. Theoretical analysis shows that minimizing the proposed loss also leads to minimizing the expected loss with both positive and negative labels. Extensive empirical evaluation on diverse graph data sets demonstrates its superior performance over existing state-of-the-art methods.

cs.LG↗

arXiv2023

Relation-aware Ensemble Learning for Knowledge Graph Embedding

Knowledge graph (KG) embedding is a fundamental task in natural language processing, and various methods have been proposed to explore semantic patterns in distinctive ways. In this paper, we propose to learn an ensemble by leveraging existing methods in a relation-aware manner. However, exploring these semantics using relation-aware ensemble leads to a much larger search space than general ensemble methods. To address this issue, we propose a divide-search-combine algorithm RelEns-DSC that searches the relation-wise ensemble weights independently. This algorithm has the same computation cost as general ensemble methods but with much better performance. Experimental results on benchmark datasets demonstrate the effectiveness of the proposed method in efficiently searching relation-aware ensemble weights and achieving state-of-the-art embedding performance. The code is public at https://github.com/LARS-research/RelEns.

cs.LG↗

arXiv2023

osmAG: Hierarchical Semantic Topometric Area Graph Maps in the OSM Format for Mobile Robotics

Maps are essential to mobile robotics tasks like localization and planning. We propose the open street map (osm) XML based Area Graph file format to store hierarchical, topometric semantic multi-floor maps of indoor and outdoor environments, since currently no such format is popular within the robotics community. Building on-top of osm we leverage the available open source editing tools and libraries of osm, while adding the needed mobile robotics aspect with building-level obstacle representation yet very compact, topometric data that facilitates planning algorithms. Through the use of common osm keys as well as custom ones we leverage the power of semantic annotation to enable various applications. For example, we support planning based on robot capabilities, to take the locomotion mode and attributes in conjunction with the environment information into account. The provided C++ library is integrated into ROS. We evaluate the performance of osmAG using real data in a global path planning application on a very big osmAG map, demonstrating its convenience and effectiveness for mobile robots.

cs.RO↗

arXiv2023

Combining Self-Supervised and Supervised Learning with Noisy Labels

Since convolutional neural networks (CNNs) can easily overfit noisy labels, which are ubiquitous in visual classification tasks, it has been a great challenge to train CNNs against them robustly. Various methods have been proposed for this challenge. However, none of them pay attention to the difference between representation and classifier learning of CNNs. Thus, inspired by the observation that classifier is more robust to noisy labels while representation is much more fragile, and by the recent advances of self-supervised representation learning (SSRL) technologies, we design a new method, i.e., CS$^3$NL, to obtain representation by SSRL without labels and train the classifier directly with noisy labels. Extensive experiments are performed on both synthetic and real benchmark datasets. Results demonstrate that the proposed method can beat the state-of-the-art ones by a large margin, especially under a high noisy level.

cs.CV↗

arXiv2023

AdaProp: Learning Adaptive Propagation for Graph Neural Network based Knowledge Graph Reasoning

Due to the popularity of Graph Neural Networks (GNNs), various GNN-based methods have been designed to reason on knowledge graphs (KGs). An important design component of GNN-based KG reasoning methods is called the propagation path, which contains a set of involved entities in each propagation step. Existing methods use hand-designed propagation paths, ignoring the correlation between the entities and the query relation. In addition, the number of involved entities will explosively grow at larger propagation steps. In this work, we are motivated to learn an adaptive propagation path in order to filter out irrelevant entities while preserving promising targets. First, we design an incremental sampling mechanism where the nearby targets and layer-wise connections can be preserved with linear complexity. Second, we design a learning-based sampling distribution to identify the semantically related entities. Extensive experiments show that our method is powerful, efficient, and semantic-aware. The code is available at https://github.com/LARS-research/AdaProp.

cs.LG↗

arXiv2022

AutoWeird: Weird Translational Scoring Function Identified by Random Search

Scoring function (SF) measures the plausibility of triplets in knowledge graphs. Different scoring functions can lead to huge differences in link prediction performances on different knowledge graphs. In this report, we describe a weird scoring function found by random search on the open graph benchmark (OGB). This scoring function, called AutoWeird, only uses tail entity and relation in a triplet to compute its plausibility score. Experimental results show that AutoWeird achieves top-1 performance on ogbl-wikikg2 data set, but has much worse performance than other methods on ogbl-biokg data set. By analyzing the tail entity distribution and evaluation protocol of these two data sets, we attribute the unexpected success of AutoWeird on ogbl-wikikg2 to inappropriate evaluation and concentrated tail entity distribution. Such results may motivate further research on how to accurately evaluate the performance of different link prediction methods for knowledge graphs.

cs.AI↗

arXiv2022

KGTuner: Efficient Hyper-parameter Search for Knowledge Graph Learning

While hyper-parameters (HPs) are important for knowledge graph (KG) learning, existing methods fail to search them efficiently. To solve this problem, we first analyze the properties of different HPs and measure the transfer ability from small subgraph to the full graph. Based on the analysis, we propose an efficient two-stage search algorithm KGTuner, which efficiently explores HP configurations on small subgraph at the first stage and transfers the top-performed configurations for fine-tuning on the large full graph at the second stage. Experiments show that our method can consistently find better HPs than the baseline algorithms within the same time budget, which achieves {9.1\%} average relative improvement for four embedding models on the large-scale KGs in open graph benchmark.

cs.LG↗

arXiv2022

Bilinear Scoring Function Search for Knowledge Graph Learning

Learning embeddings for entities and relations in knowledge graph (KG) have benefited many downstream tasks. In recent years, scoring functions, the crux of KG learning, have been human-designed to measure the plausibility of triples and capture different kinds of relations in KGs. However, as relations exhibit intricate patterns that are hard to infer before training, none of them consistently perform the best on benchmark tasks. In this paper, inspired by the recent success of automated machine learning (AutoML), we search bilinear scoring functions for different KG tasks through the AutoML techniques. However, it is non-trivial to explore domain-specific information here. We first set up a search space for AutoBLM by analyzing existing scoring functions. Then, we propose a progressive algorithm (AutoBLM) and an evolutionary algorithm (AutoBLM+), which are further accelerated by filter and predictor to deal with the domain-specific properties for KG learning. Finally, we perform extensive experiments on benchmarks in KG completion, multi-hop query, and entity classification tasks. Empirical results show that the searched scoring functions are KG dependent, new to the literature, and outperform the existing scoring functions. AutoBLM+ is better than AutoBLM as the evolutionary algorithm can flexibly explore better structures in the same budget.

cs.AI↗

arXiv2022

Knowledge Graph Reasoning with Relational Digraph

Reasoning on the knowledge graph (KG) aims to infer new facts from existing ones. Methods based on the relational path have shown strong, interpretable, and transferable reasoning ability. However, paths are naturally limited in capturing local evidence in graphs. In this paper, we introduce a novel relational structure, i.e., relational directed graph (r-digraph), which is composed of overlapped relational paths, to capture the KG's local evidence. Since the r- digraphs are more complex than paths, how to efficiently construct and effectively learn from them are challenging. Directly encoding the r-digraphs cannot scale well and capturing query-dependent information is hard in r-digraphs. We propose a variant of graph neural network, i.e., RED-GNN, to address the above challenges. Specifically, RED-GNN makes use of dynamic programming to recursively encodes multiple r-digraphs with shared edges, and utilizes a query-dependent attention mechanism to select the strongly correlated edges. We demonstrate that RED-GNN is not only efficient but also can achieve significant performance gains in both inductive and transductive reasoning tasks over existing methods. Besides, the learned attention weights in RED-GNN can exhibit interpretable evidence for KG reasoning.

cs.AI↗