Article
Computer Science, Information Systems
Xianhang Zhang, Hanchen Wang, Jianke Yu, Chen Chen, Xiaoyang Wang, Wenjie Zhang
Summary: This paper proposes a bipartite graph-based capsule network, called Bipartite Capsule Graph Neural Network (BCGNN), for bipartite graph classification task. BCGNN utilizes the capsule network and obtains information between the same type vertices in the bipartite graphs by constructing the one-mode projection. Extensive experiments on real-world datasets are conducted to demonstrate the effectiveness of the proposed method.
WORLD WIDE WEB-INTERNET AND WEB INFORMATION SYSTEMS
(2023)
Article
Computer Science, Artificial Intelligence
Zhezhe Xing, Rui Song, Yun Teng, Hao Xu
Summary: This paper proposes a dynamic heterogeneous network model for user-item bipartite networks, which utilizes dynamic heterogeneous graphs for node representation learning, and achieves outstanding results in link prediction and node classification experiments.
Article
Computer Science, Hardware & Architecture
Huichun Li, Chengli Zhao, Yangyang Liu, Xue Zhang
Summary: An anomaly detection method based on network projection is proposed, which identifies the bipartite structure of the network, constructs a projection network using cosine similarity function, and uses one-class SVM algorithm for anomaly detection. Experiments show higher precision in identifying anomalous addresses in large-scale networks.
Article
Biochemistry & Molecular Biology
Cesar A. D. Xavier, Marcio T. Godinho, Talita B. Mar, Camila G. Ferro, Osvaldo F. L. Sande, Jose C. Silva, Roberto Ramos-Sobrinho, Renato N. Nascimento, Iraildes Assuncao, Gaus S. A. Lima, Alison T. M. Lima, F. Murilo Zerbini
Summary: Several key evolutionary events have led to the emergence of geminiviruses with divided genomes, represented by the Begomovirus genus. These viruses show differential responses to evolutionary processes, with DNA-B being more permissive to variation and recombination compared to DNA-A. Despite geographic segregation, there are differences in genetic structure between DNA-A and DNA-B, belonging to distinct genetic clusters.
Article
Genetics & Heredity
Yuzhou Ma, Han Zhang, Chen Jin, Chuanze Kang
Summary: In this paper, a deep architecture called BiHo-GNN was constructed based on GNN, which integrates the properties of homogeneous and heterogeneous networks through bipartite graph embedding. BiHo-GNN can capture the mechanism of molecular association by the data encoder of heterogeneous networks. The mutual optimization between homogeneous and heterogeneous networks in BiHo-GNN promotes its robustness. BiHo-GNN outperforms existing bipartite graph-based methods in predicting lncRNA-protein interaction.
FRONTIERS IN GENETICS
(2023)
Article
Multidisciplinary Sciences
George G. G. Kennedy, William Sharpee, Alana L. L. Jacobson, Mary Wambugu, Benard Mware, Linda Hanley-Bowdoin
Summary: Cassava mosaic disease is caused by a complex of whitefly-transmitted begomoviruses, which often occur in co-infections. The disease is caused by two genome segments, DNA-A and DNA-B, which must both be transmitted by whiteflies for the infection to occur.
SCIENTIFIC REPORTS
(2023)
Article
Computer Science, Information Systems
Xianhang Zhang, Hanchen Wang, Jianke Yu, Chen Chen, Xiaoyang Wang, Wenjie Zhang
Summary: This paper proposes a polarity-based graph convolutional network (PbGCN) for sign prediction task on signed bipartite graphs. By introducing the polarity attribute and constructing one-mode projection graphs, PbGCN can effectively capture the hidden information in signed bipartite graphs.
WORLD WIDE WEB-INTERNET AND WEB INFORMATION SYSTEMS
(2022)
Article
Mathematics, Applied
Yanni Dong, Shengning Qiao, Bing Chen, Pengfei Wan, Shenggui Zhang
Summary: The study focuses on the properties of degree-based entropy in bipartite graphs and trees. The maximum degree-based entropy among bipartite graphs and trees is obtained by characterizing corresponding degree sequences.
APPLIED MATHEMATICS AND COMPUTATION
(2021)
Article
Chemistry, Analytical
Imran Baig, Najam Ul Hasan, Prajoona Valsalan, Manaf Zghaibeh
Summary: This paper presents a method for energy efficient cognitive radio-based multicast sessions by selecting the minimum possible number of relay nodes and channels, thus improving network efficiency.
Article
Computer Science, Artificial Intelligence
Jianyong Zhu, Lihong Tao, Hui Yang, Feiping Nie
Summary: Graph embedding is a widely used method for dimensionality reduction due to its computational effectiveness. However, in unsupervised graph embedding methods, the lack of labels makes it challenging to optimize the graph construction, and traditional methods become time-consuming on large-scale datasets. To address these issues, we propose Unsupervised Optimized Bipartite Graph Embedding (UOBGE), which utilizes anchor points and intrinsic graphs to preserve local and global geometric structures. Experimental results on multiple datasets validate the effectiveness and efficiency of our method.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Ecology
Hirotaka Matsumoto, Motomu Matsui
Summary: We propose a novel approach, Network-Trait association with Graph Fourier Transform (NeTaGFT), to analyze network-trait associations. NeTaGFT is inspired by graph signalling process techniques. The graph in this study corresponds to a similarity network representing the similarities between virus samples, and the graph signal corresponds to trait data. By using graph Fourier transform, NeTaGFT aims to identify trait signals and associations of various traits from a similarity network.
METHODS IN ECOLOGY AND EVOLUTION
(2023)
Article
Engineering, Multidisciplinary
Guoguang Liu
Summary: A novel ecommerce recommendation algorithm based on BGN link prediction is proposed in this paper, and experiments show that our algorithm has higher accuracy and coverage than typical recommendation algorithms.
ALEXANDRIA ENGINEERING JOURNAL
(2022)
Article
Computer Science, Information Systems
Yuli Jiang, Huaijia Lin, Ye Li, Yu Rong, Hong Cheng, Xin Huang
Summary: This paper enhances the expressive power of GCN models by utilizing node features and building a node-feature bipartite graph. It exploits the bipartite graph convolutional network to model node-feature relations and achieves more accurate predictions for each node.
INFORMATION SCIENCES
(2023)
Article
Computer Science, Artificial Intelligence
Jianyong Zhu, Xinyun Chen, Hui Yang, Feiping Nie
Summary: In traditional graph embedding methods, graph construction is sensitive to high-dimensional data with noise and outliers, and the optimization of graph construction and dimensionality reduction is disconnected. To address these problems, we propose an unsupervised dimensionality reduction method based on the bipartite graph. It captures the local structure of high-dimensional data effectively by adaptive neighbor allocation and achieves mutual optimization of graph construction and projection matrix learning.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Ecology
QinQin Yu, Matti Gralka, Marie-Cecilia Duvernoy, Megan Sousa, Arbel Harpak, Oskar Hallatschek
Summary: Demographic noise, driven by random birth and death events, reduces the efficacy of natural selection in evolution. Single gene deletion mutations decrease demographic noise, increasing the establishment probability of beneficial mutations. Demographic noise can be an evolvable trait of a population.
Review
Cell Biology
Jerome Teuliere, Debashish Bhattacharya, Eric Bapteste
AGEING RESEARCH REVIEWS
(2020)
Article
Ecology
Charles Bernard, Yanyan Li, Philippe Lopez, Eric Bapteste
Summary: The phi3T phage utilizes both the arbitrium quorum sensing system and the host-derived Rap phi-Phr phi system to communicate and coordinate lytic-to-lysogeny transitions based on population density and stress levels of the bacterial hosts. This novel QS system not only regulates host defense mechanisms during viral infection, but also provides lysogenized bacteria with a fitness advantage and delays costly production of public goods. Ultimately, this discovery sheds light on how phage communication systems contribute to phage-host evolutionary stability.
Article
Evolutionary Biology
Romain Lannes, Louise Cavaud, Philippe Lopez, Eric Bapteste
Summary: The research discovered the significant impact of marine nanoorganisms on carbon cycling and carbon fixation, with marine nanoorganisms from unknown phylogenetic lineages showing greater diversity in functionality and taxonomy.
GENOME BIOLOGY AND EVOLUTION
(2021)
Review
Cell Biology
Jerome Teuliere, Charles Bernard, Eric Bapteste
Summary: The concept of age-distorters introduces the idea that external factors such as viruses, parasites, and symbionts can carry genes that interfere with the aging process of other organisms for their own evolutionary benefit. This interference results in organismal aging by manipulating the reproduction and maintenance trade-offs of the host, leading to expanded disposable soma. The acknowledgment of age-distorters as external sources of mutation accumulation and antagonistic pleiotropic genes expands the scope of existing theories on aging and evolutionary biology.
AGEING RESEARCH REVIEWS
(2021)
Letter
Biochemistry & Molecular Biology
Andrew K. Watson, Philippe Lopez, Eric Bapteste
TRENDS IN MICROBIOLOGY
(2021)
Article
Biology
Raphael Meheust, Shuo Huang, Rafael Rivera-Lugo, Jillian F. Banfield, Samuel H. Light
Summary: A comprehensive bioinformatic analysis of 31,910 prokaryotic genomes revealed the widespread presence of extracytosolic ApbEs in bacteria and highlighted the diverse functions of flavinylation in various biochemical processes. The study identified protein classes responsible for transmembrane electron transfer and domains that are flavinylated by ApbE, as well as associations with iron reduction, assimilation, and respiratory electron transport chains. Additionally, the research discovered interspecies gene cluster variability and a potential new class of 'multi-flavinylated proteins' involved in longer distance electron transfer.
Article
Microbiology
Cindy J. Castelle, Raphael Meheust, Alexander L. Jaffe, Kiley Seitz, Xianzhe Gong, Brett J. Baker, Jillian F. Banfield
Summary: DPANN are small-celled archaea predicted to be symbionts, with proteome content revealing their relationships and potential genetic overlap with bacteria. The separation of DPANN genomes from other archaea parallels the separation of CPR bacteria from all other bacteria, indicating potential symbiosis-related functions. Pacearchaeota and Woesearchaeota, with limited metabolic capacities, show features suggesting scavenged nucleotide metabolisms and episymbiont relationships with bacteria. Additionally, some DPANN genomes contain pathways for unusual nucleotide synthesis and systems for protein refolding, indicating efficient folding of both archaeal and horizontally acquired bacterial proteins.
FRONTIERS IN MICROBIOLOGY
(2021)
Review
Biology
Eric Bapteste, Philippe Gerard, Catherine Larose, Manuel Blouin, Fabrice Not, Liliane Campos, Geraldine Aidan, M. Andre Selosse, M. Sarah Adenis, Frederic Bouchard, Sebastien Dutreuil, Eduardo Corel, Chloe Vigliotti, Philippe Huneman, F. Joseph Lapointe, Philippe Lopez
Summary: Microbiome studies are leading to an interdisciplinary epistemic revolution, influencing various fields and practices by emphasizing interactions, multi-scalar networks, and a redefinition of individuals. This ongoing revolution de-anthropocentrifies our perception of the world and could potentially unify diverse disciplines.
Article
Biochemistry & Molecular Biology
Andrew K. Watson, Philippe Lopez, Eric Bapteste
Summary: Genomes contain gene families with limited distributions, potentially representing new genes and innovations in protein-coding sequences. Some genes may have formed de novo from noncoding sequences, with processes like overprinting and out-of-frame remodeling events contributing to the origin of new gene families. Analysis on Escherichia coli genomes suggests that alternative reading frames of existing ORFs can contribute significantly to de novo genes in bacteria.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Biochemistry & Molecular Biology
Guillaume Bernard, Jerome Teuliere, Philippe Lopez, Eduardo Corel, Francois-Joseph Lapointe, Eric Bapteste
Summary: Despite identifying multiple mechanistic causes and developing evolutionary theories to understand organismal aging, empirical evidence on the timing, reasons, and mechanisms of aging is limited by phylogenetic constraints. In a natural population of a long-lived species, gene co-expression networks become more fragmented with age, indicating a decline in natural selection strength and a general dysregulation of gene co-expression in aging individuals. However, selective pressures are still strong enough to maintain specific age-related gene co-expression patterns, suggesting that older individuals from long-lived species experience a decrease in natural selection strength while being subject to targeted selection for specific biological processes.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Virginie Lemieux-Labonte, Chloe Vigliotti, Zoran Tadic, Beck Wehrle, Philippe Lopez, Eric Bapteste, Francois-Joseph Lapointe, Donovan P. German, Anthony Herrel
Summary: Dietary changes are important factors driving variation in mammalian gut microbiota composition, but other factors such as insularity and population of origin also contribute to differences in microbial composition.
Article
Multidisciplinary Sciences
Eduard Ocana-Pallares, Tom A. Williams, David Lopez-Escardo, Alicia S. Arroyo, Jananan S. Pathmanathan, Eric Bapteste, Denis Tikhonenkov, Patrick J. Keeling, Gergely J. Szollosi, Inaki Ruiz-Trillo
Summary: Animals and fungi have distinct morphologies and genetic changes. Animals gained important genes from pre-metazoan ancestors, while fungi experienced net losses in functional categories. Fungal genomes have more metabolic genes and show less divergence from the Opisthokonta ancestor compared to animals. Gene fusions are more prevalent in animals, while horizontal gene transfers are more common in fungi and protists.
Article
Biochemistry & Molecular Biology
Jerome Teuliere, Charles Bernard, Hugo Bonnefous, Johannes Martens, Philippe Lopez, Eric Bapteste
Summary: Some viruses have been experimentally shown to accelerate human aging and cellular senescence. There is a hypothesis that aging in humans may also depend on virally encoded interactions, in addition to genetic factors. Through network-based analyses, it was found that many viruses interact with proteins associated with human aging. Influenza A virus (subtype H1N1) was identified as a major candidate for manipulating cellular senescence. The findings have implications for various fields including evolutionary biology, aging study, virology, medicine, and demography.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Geriatrics & Gerontology
Jerome Teuliere, Charles Bernard, Eduardo Corel, Francois-Joseph Lapointe, Johannes Martens, Philippe Lopez, Eric Bapteste
Summary: The genetic roots of ageing and longevity variations are not well understood. Comparative analyses have identified evolutionarily conserved pathways associated with longevity or ageing. This study focused on Opisthokonta species to analyze protein interactions related to ageing or longevity, providing comprehensive understanding of the evolution of ageing and longevity pathways. The study identified key antagonistic regulators of ageing/longevity and predicted novel evolutionarily conserved longevity/ageing-related proteins in humans, which could serve as potential targets for anti-ageing treatments.
Article
Biochemistry & Molecular Biology
Eric Bapteste, Francois Papale
Summary: Doolittle and Inkpen proposed a theory that natural selection drives the sideways evolution of two different selective units - singers and songs, offering new explanations for key phenomena through selected patterns of interactions. By analyzing the interaction networks of songs and singers, a novel, actionable, inclusive, and mathematical approach is provided to analyze the reproduction, evolution, and fitness of interconnected biological and ecosystemic processes.
