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Irwin King

Publications and source records attributed to Irwin King.

At least 127 records · Page 7Linked to original sources
arXiv2024

Deep Structural Knowledge Exploitation and Synergy for Estimating Node Importance Value on Heterogeneous Information Networks

Node importance estimation problem has been studied conventionally with homogeneous network topology analysis. To deal with network heterogeneity, a few recent methods employ graph neural models to automatically learn diverse sources of information. However, the major concern revolves around that their full adaptive learning process may lead to insufficient information exploration, thereby formulating the problem as the isolated node value prediction with underperformance and less interpretability. In this work, we propose a novel learning framework: SKES. Different from previous automatic learning designs, SKES exploits heterogeneous structural knowledge to enrich the informativeness of node representations. Based on a sufficiently uninformative reference, SKES estimates the importance value for any input node, by quantifying its disparity against the reference. This establishes an interpretable node importance computation paradigm. Furthermore, SKES dives deep into the understanding that "nodes with similar characteristics are prone to have similar importance values" whilst guaranteeing that such informativeness disparity between any different nodes is orderly reflected by the embedding distance of their associated latent features. Extensive experiments on three widely-evaluated benchmarks demonstrate the performance superiority of SKES over several recent competing methods.

cs.SI↗
arXiv2024

Progress and Opportunities of Foundation Models in Bioinformatics

Bioinformatics has witnessed a paradigm shift with the increasing integration of artificial intelligence (AI), particularly through the adoption of foundation models (FMs). These AI techniques have rapidly advanced, addressing historical challenges in bioinformatics such as the scarcity of annotated data and the presence of data noise. FMs are particularly adept at handling large-scale, unlabeled data, a common scenario in biological contexts due to the time-consuming and costly nature of experimentally determining labeled data. This characteristic has allowed FMs to excel and achieve notable results in various downstream validation tasks, demonstrating their ability to represent diverse biological entities effectively. Undoubtedly, FMs have ushered in a new era in computational biology, especially in the realm of deep learning. The primary goal of this survey is to conduct a systematic investigation and summary of FMs in bioinformatics, tracing their evolution, current research status, and the methodologies employed. Central to our focus is the application of FMs to specific biological problems, aiming to guide the research community in choosing appropriate FMs for their research needs. We delve into the specifics of the problem at hand including sequence analysis, structure prediction, function annotation, and multimodal integration, comparing the structures and advancements against traditional methods. Furthermore, the review analyses challenges and limitations faced by FMs in biology, such as data noise, model explainability, and potential biases. Finally, we outline potential development paths and strategies for FMs in future biological research, setting the stage for continued innovation and application in this rapidly evolving field. This comprehensive review serves not only as an academic resource but also as a roadmap for future explorations and applications of FMs in biology.

q-bio.QM↗
arXiv2024

HiHPQ: Hierarchical Hyperbolic Product Quantization for Unsupervised Image Retrieval

Existing unsupervised deep product quantization methods primarily aim for the increased similarity between different views of the identical image, whereas the delicate multi-level semantic similarities preserved between images are overlooked. Moreover, these methods predominantly focus on the Euclidean space for computational convenience, compromising their ability to map the multi-level semantic relationships between images effectively. To mitigate these shortcomings, we propose a novel unsupervised product quantization method dubbed \textbf{Hi}erarchical \textbf{H}yperbolic \textbf{P}roduct \textbf{Q}uantization (HiHPQ), which learns quantized representations by incorporating hierarchical semantic similarity within hyperbolic geometry. Specifically, we propose a hyperbolic product quantizer, where the hyperbolic codebook attention mechanism and the quantized contrastive learning on the hyperbolic product manifold are introduced to expedite quantization. Furthermore, we propose a hierarchical semantics learning module, designed to enhance the distinction between similar and non-matching images for a query by utilizing the extracted hierarchical semantics as an additional training supervision. Experiments on benchmarks show that our proposed method outperforms state-of-the-art baselines.

cs.IR↗
arXiv2023

MECCH: Metapath Context Convolution-based Heterogeneous Graph Neural Networks

Heterogeneous graph neural networks (HGNNs) were proposed for representation learning on structural data with multiple types of nodes and edges. To deal with the performance degradation issue when HGNNs become deep, researchers combine metapaths into HGNNs to associate nodes closely related in semantics but far apart in the graph. However, existing metapath-based models suffer from either information loss or high computation costs. To address these problems, we present a novel Metapath Context Convolution-based Heterogeneous Graph Neural Network (MECCH). MECCH leverages metapath contexts, a new kind of graph structure that facilitates lossless node information aggregation while avoiding any redundancy. Specifically, MECCH applies three novel components after feature preprocessing to extract comprehensive information from the input graph efficiently: (1) metapath context construction, (2) metapath context encoder, and (3) convolutional metapath fusion. Experiments on five real-world heterogeneous graph datasets for node classification and link prediction show that MECCH achieves superior prediction accuracy compared with state-of-the-art baselines with improved computational efficiency.

cs.LG↗
arXiv2023

An Augmented Index-based Efficient Community Search for Large Directed Graphs

Given a graph G and a query vertex q, the topic of community search (CS), aiming to retrieve a dense subgraph of G containing q, has gained much attention. Most existing works focus on undirected graphs which overlooks the rich information carried by the edge directions. Recently, the problem of community search over directed graphs (or CSD problem) has been studied; it finds a connected subgraph containing q, where the in-degree and out-degree of each vertex within the subgraph are at least k and l, respectively. However, existing solutions are inefficient, especially on large graphs. To tackle this issue, in this paper, we propose a novel index called D-Forest, which allows a CSD query to be completed within the optimal time cost. We further propose efficient index construction methods. Extensive experiments on six real large graphs show that our index-based query algorithm is up to two orders of magnitude faster than existing solutions.

cs.DB↗
arXiv2023

Generalized Category Discovery with Clustering Assignment Consistency

Generalized category discovery (GCD) is a recently proposed open-world task. Given a set of images consisting of labeled and unlabeled instances, the goal of GCD is to automatically cluster the unlabeled samples using information transferred from the labeled dataset. The unlabeled dataset comprises both known and novel classes. The main challenge is that unlabeled novel class samples and unlabeled known class samples are mixed together in the unlabeled dataset. To address the GCD without knowing the class number of unlabeled dataset, we propose a co-training-based framework that encourages clustering consistency. Specifically, we first introduce weak and strong augmentation transformations to generate two sufficiently different views for the same sample. Then, based on the co-training assumption, we propose a consistency representation learning strategy, which encourages consistency between feature-prototype similarity and clustering assignment. Finally, we use the discriminative embeddings learned from the semi-supervised representation learning process to construct an original sparse network and use a community detection method to obtain the clustering results and the number of categories simultaneously. Extensive experiments show that our method achieves state-of-the-art performance on three generic benchmarks and three fine-grained visual recognition datasets. Especially in the ImageNet-100 data set, our method significantly exceeds the best baseline by 15.5\% and 7.0\% on the \texttt{Novel} and \texttt{All} classes, respectively.

cs.CV↗
arXiv2023

Momentum Contrastive Pre-training for Question Answering

Existing pre-training methods for extractive Question Answering (QA) generate cloze-like queries different from natural questions in syntax structure, which could overfit pre-trained models to simple keyword matching. In order to address this problem, we propose a novel Momentum Contrastive pRe-training fOr queStion anSwering (MCROSS) method for extractive QA. Specifically, MCROSS introduces a momentum contrastive learning framework to align the answer probability between cloze-like and natural query-passage sample pairs. Hence, the pre-trained models can better transfer the knowledge learned in cloze-like samples to answering natural questions. Experimental results on three benchmarking QA datasets show that our method achieves noticeable improvement compared with all baselines in both supervised and zero-shot scenarios.

cs.CL↗
arXiv2023

Large Language Models as Source Planner for Personalized Knowledge-grounded Dialogue

Open-domain dialogue system usually requires different sources of knowledge to generate more informative and evidential responses. However, existing knowledge-grounded dialogue systems either focus on a single knowledge source or overlook the dependency between multiple sources of knowledge, which may result in generating inconsistent or even paradoxical responses. To incorporate multiple knowledge sources and dependencies between them, we propose SAFARI, a novel framework that leverages the exceptional capabilities of large language models (LLMs) in planning, understanding, and incorporating under both supervised and unsupervised settings. Specifically, SAFARI decouples the knowledge grounding into multiple sources and response generation, which allows easy extension to various knowledge sources including the possibility of not using any sources. To study the problem, we construct a personalized knowledge-grounded dialogue dataset \textit{\textbf{K}nowledge \textbf{B}ehind \textbf{P}ersona}~(\textbf{KBP}), which is the first to consider the dependency between persona and implicit knowledge. Experimental results on the KBP dataset demonstrate that the SAFARI framework can effectively produce persona-consistent and knowledge-enhanced responses.

cs.CL↗
arXiv2023

ResNorm: Tackling Long-tailed Degree Distribution Issue in Graph Neural Networks via Normalization

Graph Neural Networks (GNNs) have attracted much attention due to their ability in learning representations from graph-structured data. Despite the successful applications of GNNs in many domains, the optimization of GNNs is less well studied, and the performance on node classification heavily suffers from the long-tailed node degree distribution. This paper focuses on improving the performance of GNNs via normalization. In detail, by studying the long-tailed distribution of node degrees in the graph, we propose a novel normalization method for GNNs, which is termed ResNorm (\textbf{Res}haping the long-tailed distribution into a normal-like distribution via \textbf{norm}alization). The $scale$ operation of ResNorm reshapes the node-wise standard deviation (NStd) distribution so as to improve the accuracy of tail nodes (\textit{i}.\textit{e}., low-degree nodes). We provide a theoretical interpretation and empirical evidence for understanding the mechanism of the above $scale$. In addition to the long-tailed distribution issue, over-smoothing is also a fundamental issue plaguing the community. To this end, we analyze the behavior of the standard shift and prove that the standard shift serves as a preconditioner on the weight matrix, increasing the risk of over-smoothing. With the over-smoothing issue in mind, we design a $shift$ operation for ResNorm that simulates the degree-specific parameter strategy in a low-cost manner. Extensive experiments have validated the effectiveness of ResNorm on several node classification benchmark datasets.

cs.LG↗
arXiv2023

kHGCN: Tree-likeness Modeling via Continuous and Discrete Curvature Learning

The prevalence of tree-like structures, encompassing hierarchical structures and power law distributions, exists extensively in real-world applications, including recommendation systems, ecosystems, financial networks, social networks, etc. Recently, the exploitation of hyperbolic space for tree-likeness modeling has garnered considerable attention owing to its exponential growth volume. Compared to the flat Euclidean space, the curved hyperbolic space provides a more amenable and embeddable room, especially for datasets exhibiting implicit tree-like architectures. However, the intricate nature of real-world tree-like data presents a considerable challenge, as it frequently displays a heterogeneous composition of tree-like, flat, and circular regions. The direct embedding of such heterogeneous structures into a homogeneous embedding space (i.e., hyperbolic space) inevitably leads to heavy distortions. To mitigate the aforementioned shortage, this study endeavors to explore the curvature between discrete structure and continuous learning space, aiming at encoding the message conveyed by the network topology in the learning process, thereby improving tree-likeness modeling. To the end, a curvature-aware hyperbolic graph convolutional neural network, \{kappa}HGCN, is proposed, which utilizes the curvature to guide message passing and improve long-range propagation. Extensive experiments on node classification and link prediction tasks verify the superiority of the proposal as it consistently outperforms various competitive models by a large margin.

cs.LG↗
arXiv2023

Diagnose Like a Pathologist: Transformer-Enabled Hierarchical Attention-Guided Multiple Instance Learning for Whole Slide Image Classification

Multiple Instance Learning (MIL) and transformers are increasingly popular in histopathology Whole Slide Image (WSI) classification. However, unlike human pathologists who selectively observe specific regions of histopathology tissues under different magnifications, most methods do not incorporate multiple resolutions of the WSIs, hierarchically and attentively, thereby leading to a loss of focus on the WSIs and information from other resolutions. To resolve this issue, we propose a Hierarchical Attention-Guided Multiple Instance Learning framework to fully exploit the WSIs. This framework can dynamically and attentively discover the discriminative regions across multiple resolutions of the WSIs. Within this framework, an Integrated Attention Transformer is proposed to further enhance the performance of the transformer and obtain a more holistic WSI (bag) representation. This transformer consists of multiple Integrated Attention Modules, which is the combination of a transformer layer and an aggregation module that produces a bag representation based on every instance representation in that bag. The experimental results show that our method achieved state-of-the-art performances on multiple datasets, including Camelyon16, TCGA-RCC, TCGA-NSCLC, and an in-house IMGC dataset. The code is available at https://github.com/BearCleverProud/HAG-MIL.

cs.CV↗
arXiv2023

A Unified View of Deep Learning for Reaction and Retrosynthesis Prediction: Current Status and Future Challenges

Reaction and retrosynthesis prediction are fundamental tasks in computational chemistry that have recently garnered attention from both the machine learning and drug discovery communities. Various deep learning approaches have been proposed to tackle these problems, and some have achieved initial success. In this survey, we conduct a comprehensive investigation of advanced deep learning-based models for reaction and retrosynthesis prediction. We summarize the design mechanisms, strengths, and weaknesses of state-of-the-art approaches. Then, we discuss the limitations of current solutions and open challenges in the problem itself. Finally, we present promising directions to facilitate future research. To our knowledge, this paper is the first comprehensive and systematic survey that seeks to provide a unified understanding of reaction and retrosynthesis prediction.

cs.LG↗
arXiv2023

GDA: Generative Data Augmentation Techniques for Relation Extraction Tasks

Relation extraction (RE) tasks show promising performance in extracting relations from two entities mentioned in sentences, given sufficient annotations available during training. Such annotations would be labor-intensive to obtain in practice. Existing work adopts data augmentation techniques to generate pseudo-annotated sentences beyond limited annotations. These techniques neither preserve the semantic consistency of the original sentences when rule-based augmentations are adopted, nor preserve the syntax structure of sentences when expressing relations using seq2seq models, resulting in less diverse augmentations. In this work, we propose a dedicated augmentation technique for relational texts, named GDA, which uses two complementary modules to preserve both semantic consistency and syntax structures. We adopt a generative formulation and design a multi-tasking solution to achieve synergies. Furthermore, GDA adopts entity hints as the prior knowledge of the generative model to augment diverse sentences. Experimental results in three datasets under a low-resource setting showed that GDA could bring {\em 2.0\%} F1 improvements compared with no augmentation technique. Source code and data are available.

cs.CL↗
arXiv2023

Hyperbolic Representation Learning: Revisiting and Advancing

The non-Euclidean geometry of hyperbolic spaces has recently garnered considerable attention in the realm of representation learning. Current endeavors in hyperbolic representation largely presuppose that the underlying hierarchies can be automatically inferred and preserved through the adaptive optimization process. This assumption, however, is questionable and requires further validation. In this work, we first introduce a position-tracking mechanism to scrutinize existing prevalent \hlms, revealing that the learned representations are sub-optimal and unsatisfactory. To address this, we propose a simple yet effective method, hyperbolic informed embedding (HIE), by incorporating cost-free hierarchical information deduced from the hyperbolic distance of the node to origin (i.e., induced hyperbolic norm) to advance existing \hlms. The proposed method HIE is both task-agnostic and model-agnostic, enabling its seamless integration with a broad spectrum of models and tasks. Extensive experiments across various models and different tasks demonstrate the versatility and adaptability of the proposed method. Remarkably, our method achieves a remarkable improvement of up to 21.4\% compared to the competing baselines.

cs.LG↗
arXiv2023

Doubly Stochastic Graph-based Non-autoregressive Reaction Prediction

Organic reaction prediction is a critical task in drug discovery. Recently, researchers have achieved non-autoregressive reaction prediction by modeling the redistribution of electrons, resulting in state-of-the-art top-1 accuracy, and enabling parallel sampling. However, the current non-autoregressive decoder does not satisfy two essential rules of electron redistribution modeling simultaneously: the electron-counting rule and the symmetry rule. This violation of the physical constraints of chemical reactions impairs model performance. In this work, we propose a new framework called that combines two doubly stochastic self-attention mappings to obtain electron redistribution predictions that follow both constraints. We further extend our solution to a general multi-head attention mechanism with augmented constraints. To achieve this, we apply Sinkhorn's algorithm to iteratively update self-attention mappings, which imposes doubly conservative constraints as additional informative priors on electron redistribution modeling. We theoretically demonstrate that our can simultaneously satisfy both rules, which the current decoder mechanism cannot do. Empirical results show that our approach consistently improves the predictive performance of non-autoregressive models and does not bring an unbearable additional computational cost.

physics.chem-ph↗
arXiv2023

Multimodal Relation Extraction with Cross-Modal Retrieval and Synthesis

Multimodal relation extraction (MRE) is the task of identifying the semantic relationships between two entities based on the context of the sentence image pair. Existing retrieval-augmented approaches mainly focused on modeling the retrieved textual knowledge, but this may not be able to accurately identify complex relations. To improve the prediction, this research proposes to retrieve textual and visual evidence based on the object, sentence, and whole image. We further develop a novel approach to synthesize the object-level, image-level, and sentence-level information for better reasoning between the same and different modalities. Extensive experiments and analyses show that the proposed method is able to effectively select and compare evidence across modalities and significantly outperforms state-of-the-art models.

cs.CL↗
arXiv2023

FedHGN: A Federated Framework for Heterogeneous Graph Neural Networks

Heterogeneous graph neural networks (HGNNs) can learn from typed and relational graph data more effectively than conventional GNNs. With larger parameter spaces, HGNNs may require more training data, which is often scarce in real-world applications due to privacy regulations (e.g., GDPR). Federated graph learning (FGL) enables multiple clients to train a GNN collaboratively without sharing their local data. However, existing FGL methods mainly focus on homogeneous GNNs or knowledge graph embeddings; few have considered heterogeneous graphs and HGNNs. In federated heterogeneous graph learning, clients may have private graph schemas. Conventional FL/FGL methods attempting to define a global HGNN model would violate schema privacy. To address these challenges, we propose FedHGN, a novel and general FGL framework for HGNNs. FedHGN adopts schema-weight decoupling to enable schema-agnostic knowledge sharing and employs coefficients alignment to stabilize the training process and improve HGNN performance. With better privacy preservation, FedHGN consistently outperforms local training and conventional FL methods on three widely adopted heterogeneous graph datasets with varying client numbers. The code is available at https://github.com/cynricfu/FedHGN .

cs.LG↗
arXiv2023

WSFE: Wasserstein Sub-graph Feature Encoder for Effective User Segmentation in Collaborative Filtering

Maximizing the user-item engagement based on vectorized embeddings is a standard procedure of recent recommender models. Despite the superior performance for item recommendations, these methods however implicitly deprioritize the modeling of user-wise similarity in the embedding space; consequently, identifying similar users is underperforming, and additional processing schemes are usually required otherwise. To avoid thorough model re-training, we propose WSFE, a model-agnostic and training-free representation encoder, to be flexibly employed on the fly for effective user segmentation. Underpinned by the optimal transport theory, the encoded representations from WSFE present a matched user-wise similarity/distance measurement between the realistic and embedding space. We incorporate WSFE into six state-of-the-art recommender models and conduct extensive experiments on six real-world datasets. The empirical analyses well demonstrate the superiority and generality of WSFE to fuel multiple downstream tasks with diverse underlying targets in recommendation.

cs.IR↗