Graph Contrastive Learning (GCL) generates graph-level embeddings by maximizing Mutual Information between different augmented views of the same graph (positive pairs), and shows promising performance in graph representation learning (GRL) without the supervision of manual annotations. However, GCL suffers from a dimensional collapse problem, i.e., embedding vectors reside in a restricted low-dimensional subspace, curtailing the expressiveness of certain embedding dimensions. In this paper, we present a theoretical analysis identifying the smoothing effect of graph pooling and graph convolution's implicit regularization as principal causes of dimension collapse in graph contrastive learning. To mitigate the above effects, we propose a Non-Maximum Removal Graph Contrastive Learning (nmrGCL) approach, which removes "prominent" dimensions (those significantly contributing to the similarity measure) for positive pairs within the pretext task. Comprehensive experiments on multiple benchmark datasets are conducted and the results show that the proposed nmrGCL outperforms the state-of-the-art methods.
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http://dx.doi.org/10.1016/j.neunet.2024.106652 | DOI Listing |
Genetics
January 2025
Max Planck Research Group Behavioural Genomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Straße 2, 24306 Plön, Germany.
Multiple methods of demography inference are based on the ancestral recombination graph. This powerful approach uses observed mutations to model local genealogies changing along chromosomes by historical recombination events. However, inference of underlying genealogies is difficult in regions with high recombination rate relative to mutation rate due to the lack of mutations representing genealogies.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Ecole Nationale Supérieure de Chimie de Paris, Université PSL, CNRS, Institute of Chemistry for Life and Health Sciences, 75 005 Paris, France.
In this contribution, we examine the interplay between target definition, data distribution, featurization approaches, and model architectures on graph-based deep learning models for thermodynamic property prediction. Through consideration of five curated data sets, exhibiting diversity in elemental composition, multiplicity, charge state, and size, we examine the impact of each of these factors on model accuracy. We observe that target definition, i.
View Article and Find Full Text PDFKorean J Radiol
January 2025
Research Scientist, AIRS Medical Inc., Seoul, Republic of Korea.
Objective: To evaluate the clinical efficacy of ultrafast dynamic contrast-enhanced (DCE)-MRI using a compressed sensing (CS) technique for differentiating benign and malignant soft-tissue tumors (STTs) and to evaluate the factors related to the grading of malignant STTs.
Materials And Methods: A total of 165 patients (96 male; mean age, 61 years), comprising 111 with malignant STTs and 54 with benign STTs according to the 2020 WHO classification, underwent DCE-MRI with CS between June 2018 and June 2023. The clinical, qualitative, and quantitative parameters associated with conventional MRI were also obtained.
Neural Netw
January 2025
Chongqing Key Laboratory of Computational Intelligence, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China; College of Computer and Information Science, Chongqing Normal University, Chongqing, 401331, China. Electronic address:
The production of expressive molecular representations with scarce labeled data is challenging for AI-driven drug discovery. Mainstream studies often follow a pipeline that pre-trains a specific molecular encoder and then fine-tunes it. However, the significant challenges of these methods are (1) neglecting the propagation of diverse information within molecules and (2) the absence of knowledge and chemical constraints in the pre-training strategy.
View Article and Find Full Text PDFMol Inform
January 2025
Faculty of Information Technology, HUTECH University, 700000, Ho Chi Minh City, Vietnam.
In recent times, graph representation learning has been becoming a hot research topic which has attracted a lot of attention from researchers. Graph embeddings have diverse applications across fields such as information and social network analysis, bioinformatics and cheminformatics, natural language processing (NLP), and recommendation systems. Among the advanced deep learning (DL) based architectures used in graph representation learning, graph neural networks (GNNs) have emerged as the dominant and highly effective framework.
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