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Two new organo-inorganic hybrids, (C2N2H10)[Cu(H2O)4](BeF4)2 (1) and (C2N2H10)[Cu(H2O)4](SeO4)2 (2), were prepared via the interaction of ethylenediamine, copper fluoroberyllate or selenate, and H2[BeF4]/H2SeO4 in aqueous solutions. The structures of 1 and 2 are similar to each other and the previously reported (C2N2H10)[Cu(H2O)4](SO4)2: monoclinic, P21/c, a = 5.1044(2) Å, b = 11.6171(4) Å, c = 10.1178(3) Å, and β = 94.431(3)° for 1; and a = 5.25020(10), b = 11.7500(2), c = 10.4434(2), and β = 94.5464(17)° for 2. All structures contain a square planar [Cu(H2O)4]2+ species, which coordinates, at rather long distances, two TX42− tetrahedral dianions in κ1 mode, forming relatively weak [Cu(H2O)4(TX4)2]2− complexes. These are linked together via hydrogen bonding into pseudo-chains; the ethylenediammonium cations link them into a 3D architecture. Compound 1 is, to the best of our knowledge, the first—though expected—representative of a hybrid organo-inorganic fluoroberyllate. The crystal chemical relations within the structural family (enH2)[Cu(H2O)4](TX4)2 are discussed. [ABSTRACT FROM AUTHOR]

Graph-theory-based topological impairment of the whole-brain network has been verified to be one of the characteristics of mild cognitive impairment (MCI). However, two major challenges impede the further understanding of topological features for the personalized functional connectivity network of early Parkinson's disease (ePD) with MCI. The uncertain of characteristic frequency band reflecting the abnormality of ePD-MCI and the setting of fixed length of sliding window at a second level in the construction of conventional brain network both limit a deeper exploration of network characteristics for ePD-MCI. Thus, a convolutional neural network is constructed first and the gradient-weighted class activation mapping method is used to determine the characteristic frequency band of the ePD-MCI. It is found that 1–4 Hz is a characteristic frequency band for recognizing MCI in ePD. Then, we propose a microstate window construction method based on electroencephalography microstate sequences to build brain functional network. By exploring the graph-theory-based topological features and their clinical correlations with cognitive impairment, it is shown that the clustering coefficient, global efficiency, and local efficiency of the occipital lobe significantly decrease in ePD-MCI, which reflects the low degree of nodes interconnection, low efficiency of parallel information transmission and low communication efficiency among the nodes in the brain network of the occipital lobe may be the neural marker of ePD-MCI. The finding of personalized topological impairments of the brain network may be a potential characteristic of early PD-MCI. [ABSTRACT FROM AUTHOR]

Host-pathogen interactions (HPIs) are vital in numerous biological activities and are intrinsically linked to the onset and progression of infectious diseases. HPIs are pivotal in the entire lifecycle of diseases: from the onset of pathogen introduction, navigating through the mechanisms that bypass host cellular defenses, to its subsequent proliferation inside the host. At the heart of these stages lies the synergy of proteins from both the host and the pathogen. By understanding these interlinking protein dynamics, we can gain crucial insights into how diseases progress and pave the way for stronger plant defenses and the swift formulation of countermeasures. In the framework of current study, we developed a web-based R/Shiny app, Deep-HPI-pred, that uses network-driven feature learning method to predict the yet unmapped interactions between pathogen and host proteins. Leveraging citrus and CLas bacteria training datasets as case study, we spotlight the effectiveness of Deep-HPI-pred in discerning Protein-protein interaction (PPIs) between them. Deep-HPI-pred use Multilayer Perceptron (MLP) models for HPI prediction, which is based on a comprehensive evaluation of topological features and neural network architectures. When subjected to independent validation datasets, the predicted models consistently surpassed a Matthews correlation coefficient (MCC) of 0.80 in host-pathogen interactions. Remarkably, the use of Eigenvector Centrality as the leading topological feature further enhanced this performance. Further, Deep-HPI-pred also offers relevant gene ontology (GO) term information for each pathogen and host protein within the system. This protein annotation data contributes an additional layer to our understanding of the intricate dynamics within host-pathogen interactions. In the additional benchmarking studies, the Deep-HPI-pred model has proven its robustness by consistently delivering reliable results across different host-pathogen systems, including plant-pathogens (accuracy of 98.4% and 97.9%), human-virus (accuracy of 94.3%), and animal-bacteria (accuracy of 96.6%) interactomes. These results not only demonstrate the model's versatility but also pave the way for gaining comprehensive insights into the molecular underpinnings of complex host-pathogen interactions. Taken together, the Deep-HPI-pred applet offers a unified web service for both identifying and illustrating interaction networks. Deep-HPI-pred applet is freely accessible at its homepage: https://cbi.gxu.edu.cn/shiny-apps/Deep-HPI-pred/ and at github: https://github.com/tahirulqamar/Deep-HPI-pred.

Abstract The nonlinear progression of COVID-19 positive cases, their fluctuations, the correlations in amplitudes and phases across different regions, along with seasonality or periodicity, pose challenges to thoroughly examining the data for revealing similarities or detecting anomalous trajectories. To address this, we conducted a nonlinear time series analysis combining wavelet and persistent homology to detect the qualitative properties underlying COVID-19 daily infection numbers at the state level from the pandemic’s onset to June 2024 in Malaysia. The first phase involved investigating the evolution of daily confirmed cases by state in the time-frequency domain using wavelets. Subsequently, a topological feature-based time series clustering is performed by reconstructing a higher-dimensional phase space through a delay embedding method. Our findings reveal a prominent 7-day periodicity in case numbers from mid-2021 to the end of 2022. The state-wise daily cases are moderately correlated in both amplitudes and phases during the Delta and Omicron waves. Biweekly averaged data significantly enhances the detection of topological loops associated with these waves. Selangor demonstrates unique case trajectories, while Pahang shows the highest similarity with other states. This methodological framework provides a more detailed understanding of epidemiological time series data, offering valuable insights for preparing for future public health crises.

Topology optimization is crucial for the mechanical design of vehicles and aircraft, allowing changes in the shape of structures and the placement of features. Recent advances have integrated deep generative models, particularly convolutional neural networks, to streamline this process.to streamline this process. However, these models struggle to preserve subtle structural features. To overcome these limitations, this study introduced a generative model adept at identifying the topological features inherent in real shapes, such as connectivity and holes, to enhance the effectiveness of topology optimization. A conditional variational autoencoder (CVAE) was employed to predict both the shape and compliance simultaneously. This model, CVAE with persistent homology, generates optimal material distributions by considering topological properties. The learning process introduced a term that minimizes the difference in topological features between true and reconstructed shapes. The proposed model can generate optimal material distributions by considering topological properties, eliminating the need for iterative calculations. This approach was validated using two numerical examples. The accuracy of the generated material distributions was compared with conventional methods using the mean-squared error. An average improvement in accuracy of approximately 36.85% was observed across the two results. This confirms that shapes considering compliance and connectivity can be accurately predicted. [ABSTRACT FROM AUTHOR]

In the realm of underwater environment detection, achieving information matching stands as a pivotal step, forming an indispensable component for collaborative detection and research in areas such as distributed mapping. Nevertheless, the progress in studying the matching of underwater side-scan sonar images has been hindered by challenges including low image quality, intricate features, and susceptibility to distortion in commonly used side-scan sonar images. This article presents a comprehensive overview of the advancements in underwater sonar image processing. Building upon the novel SchemaNet image topological structure extraction model, we introduce a feature matching model grounded in side-scan sonar images. The proposed approach employs a semantic segmentation network as a teacher model to distill the DeiT model during training, extracting the attention matrix of intermediate layer outputs. This emulates SchemaNet's transformation method, enabling the acquisition of high-dimensional topological structure features from the image. Subsequently, utilizing a real side-scan sonar dataset and augmenting data, we formulate a matching dataset and train the model using a graph neural network. The resulting model demonstrates effective performance in side-scan sonar image matching tasks. These research findings bear significance for underwater detection and target recognition and can offer valuable insights and references for image processing in diverse domains. [ABSTRACT FROM AUTHOR]

Two new organo-inorganic hybrids, (C2N2H10)[Cu(H2O)4](BeF4)2 (1) and (C2N2H10)[Cu(H2O)4](SeO4)2 (2), were prepared via the interaction of ethylenediamine, copper fluoroberyllate or selenate, and H2[BeF4]/H2SeO4 in aqueous solutions. The structures of 1 and 2 are similar to each other and the previously reported (C2N2H10)[Cu(H2O)4](SO4)2: monoclinic, P21/c, a = 5.1044(2) Å, b = 11.6171(4) Å, c = 10.1178(3) Å, and β = 94.431(3)° for 1; and a = 5.25020(10), b = 11.7500(2), c = 10.4434(2), and β = 94.5464(17)° for 2. All structures contain a square planar [Cu(H2O)4]2+ species, which coordinates, at rather long distances, two TX42− tetrahedral dianions in κ1 mode, forming relatively weak [Cu(H2O)4(TX4)2]2− complexes. These are linked together via hydrogen bonding into pseudo-chains; the ethylenediammonium cations link them into a 3D architecture. Compound 1 is, to the best of our knowledge, the first—though expected—representative of a hybrid organo-inorganic fluoroberyllate. The crystal chemical relations within the structural family (enH2)[Cu(H2O)4](TX4)2 are discussed.

Investigating the time–frequency-based phase synchronization between nonstationary time series of the cryptocurrencies' prices can be a suitable tool to reveal their complicated interactions at different frequencies. In this work, the phase synchronization between 25 cryptocurrencies with the highest capitalization from December 1, 2021 to June 1, 2022 is calculated using the phase-locking value method based on wavelet transform. Then, utilizing the graph theory, the cryptocurrency networks are constructed, and their topological features like path length (PL), clustering coefficient (CC) and node strength are evaluated in various frequencies. This research indicates a strong phase synchronization between the investigated cryptocurrencies, especially in low frequencies. Also, the networks' high average CC and short PL compared to their equivalent regular and random networks display the small-worldness of the networks. We observe from the obtained results that Bitcoin, Ethereum and Binance currencies, among the most popular cryptocurrencies, have the highest average node strengths at different frequencies. Also, TRON shows the lowest CC and node strength among all currencies, representing its limited phase interaction with other currencies. [ABSTRACT FROM AUTHOR]

Abstract Background Automatic and accurate extraction of diverse biomedical relations from literature is a crucial component of bio-medical text mining. Currently, stacking various classification networks on pre-trained language models to perform fine-tuning is a common framework to end-to-end solve the biomedical relation extraction (BioRE) problem. However, the sequence-based pre-trained language models underutilize the graphical topology of language to some extent. In addition, sequence-oriented deep neural networks have limitations in processing graphical features. Results In this paper, we propose a novel method for sentence-level BioRE task, BioEGRE (BioELECTRA and Graph pointer neural net-work for Relation Extraction), aimed at leveraging the linguistic topological features. First, the biomedical literature is preprocessed to retain sentences involving pre-defined entity pairs. Secondly, SciSpaCy is employed to conduct dependency parsing; sentences are modeled as graphs based on the parsing results; BioELECTRA is utilized to generate token-level representations, which are modeled as attributes of nodes in the sentence graphs; a graph pointer neural network layer is employed to select the most relevant multi-hop neighbors to optimize representations; a fully-connected neural network layer is employed to generate the sentence-level representation. Finally, the Softmax function is employed to calculate the probabilities. Our proposed method is evaluated on three BioRE tasks: a multi-class (CHEMPROT) and two binary tasks (GAD and EU-ADR). The results show that our method achieves F1-scores of 79.97% (CHEMPROT), 83.31% (GAD), and 83.51% (EU-ADR), surpassing the performance of existing state-of-the-art models. Conclusion The experimental results on 3 biomedical benchmark datasets demonstrate the effectiveness and generalization of BioEGRE, which indicates that linguistic topology and a graph pointer neural network layer explicitly improve performance for BioRE tasks.

Background: Automatic and accurate extraction of diverse biomedical relations from literature is a crucial component of bio-medical text mining. Currently, stacking various classification networks on pre-trained language models to perform fine-tuning is a common framework to end-to-end solve the biomedical relation extraction (BioRE) problem. However, the sequence-based pre-trained language models underutilize the graphical topology of language to some extent. In addition, sequence-oriented deep neural networks have limitations in processing graphical features. Results: In this paper, we propose a novel method for sentence-level BioRE task, BioEGRE (BioELECTRA and Graph pointer neural net-work for Relation Extraction), aimed at leveraging the linguistic topological features. First, the biomedical literature is preprocessed to retain sentences involving pre-defined entity pairs. Secondly, SciSpaCy is employed to conduct dependency parsing; sentences are modeled as graphs based on the parsing results; BioELECTRA is utilized to generate token-level representations, which are modeled as attributes of nodes in the sentence graphs; a graph pointer neural network layer is employed to select the most relevant multi-hop neighbors to optimize representations; a fully-connected neural network layer is employed to generate the sentence-level representation. Finally, the Softmax function is employed to calculate the probabilities. Our proposed method is evaluated on three BioRE tasks: a multi-class (CHEMPROT) and two binary tasks (GAD and EU-ADR). The results show that our method achieves F1-scores of 79.97% (CHEMPROT), 83.31% (GAD), and 83.51% (EU-ADR), surpassing the performance of existing state-of-the-art models. Conclusion: The experimental results on 3 biomedical benchmark datasets demonstrate the effectiveness and generalization of BioEGRE, which indicates that linguistic topology and a graph pointer neural network layer explicitly improve performance for BioRE tasks. [ABSTRACT FROM AUTHOR]

Background: Corneal fluorescein staining is a key biomarker in evaluating dry eye disease. However, subjective scales of corneal fluorescein staining are lacking in consistency and increase the difficulties of an accurate diagnosis for clinicians. This study aimed to propose an automatic machine learning-based method for corneal fluorescein staining evaluation by utilizing prior information about the spatial connection and distribution of the staining region. Methods: We proposed an end-to-end automatic machine learning-based classification model that consists of staining region identification, feature signature construction, and machine learning-based classification, which fully scrutinizes the multiscale topological features together with conventional texture and morphological features. The proposed model was evaluated using retrospective data from Beijing Tongren Hospital. Two masked ophthalmologists scored images independently using the Sjögren's International Collaborative Clinical Alliance Ocular Staining Score scale. Results: A total of 382 images were enrolled in the study. A signature with six topological features, two textural features, and two morphological features was constructed after feature extraction and selection. Support vector machines showed the best classification performance (accuracy: 82.67%, area under the curve: 96.59%) with the designed signature. Meanwhile, topological features contributed more to the classification, compared with other features. According to the distribution and correlation with features and scores, topological features performed better than others. Conclusions: An automatic machine learning-based method was advanced for corneal fluorescein staining evaluation. The topological features in presenting the spatial connectivity and distribution of staining regions are essential for an efficient corneal fluorescein staining evaluation. This result implies the clinical application of topological features in dry-eye diagnosis and therapeutic effect evaluation. [ABSTRACT FROM AUTHOR]

In the realm of underwater environment detection, achieving information matching stands as a pivotal step, forming an indispensable component for collaborative detection and research in areas such as distributed mapping. Nevertheless, the progress in studying the matching of underwater side-scan sonar images has been hindered by challenges including low image quality, intricate features, and susceptibility to distortion in commonly used side-scan sonar images. This article presents a comprehensive overview of the advancements in underwater sonar image processing. Building upon the novel SchemaNet image topological structure extraction model, we introduce a feature matching model grounded in side-scan sonar images. The proposed approach employs a semantic segmentation network as a teacher model to distill the DeiT model during training, extracting the attention matrix of intermediate layer outputs. This emulates SchemaNet’s transformation method, enabling the acquisition of high-dimensional topological structure features from the image. Subsequently, utilizing a real side-scan sonar dataset and augmenting data, we formulate a matching dataset and train the model using a graph neural network. The resulting model demonstrates effective performance in side-scan sonar image matching tasks. These research findings bear significance for underwater detection and target recognition and can offer valuable insights and references for image processing in diverse domains.

Abstract Classical magnetic fields might change the properties of topological insulators such as the time reversal symmetry protected topological edge states. This poses a question that whether quantized fields would change differently the feature of topological materials with respect to the classical one. In this paper, we propose a model to describe topological insulators (ultracold atoms in square optical lattices with magnetic field) coupled to a tunable single-mode quantized field, and discuss the topological features of the system. We find that the quantized field can induce topological quantum phase transitions in a different way. To be specific, for fixed gauge magnetic flux ratio, we calculate the energy bands for different coupling constants between the systems and the fields in both open and periodic boundary conditions. We find that the Hofstadter butterfly graph is divided into a pair for continuous gauge magnetic flux ratio, which is different from the one without single-mode quantized field. In addition, we plot topological phase diagrams characterized by Chern number as a function of the momentum of the single-mode quantized field and obtain a quantized structure with non-zero filling factor.

A new method for decomposing an image into separate objects of interest is proposed in the article. The developed method is based on the use of persistent homology. A process of direct and reverse image transformation is shown. Following direct transformation, the original image is represented as a set of matrices that can be divided into basic and detailing ones. The basic matrices contain information about the basic structure of objects in the images, and the detailing ones include data about the details of these objects, about small objects or the noise component. It is shown that there is a certain analogy with the Wavelet transformation, but the proposed method is based on a fundamentally different theoretical basis. A numerical example reflecting the basic essence of the method is described in detail. Properties of the decomposition and the possibility of using standard algebraic operations on decomposition matrices are described. The reverse transformation allows us to take into account the changed properties of individual objects and synthesize a new image. Prospects of using the proposed decomposition for solving practical problems are demonstrated. Algorithms have been developed for binarization of images and removal of text on a non-uniform background. Data analysis and processing is carried out using a unified approach in the space of decomposition matrices. The results of binarization have shown that, when compared with analogues, the developed algorithm will perform better when the binarization is used to isolate a multitude of individual objects. The obtained results of the algorithm for deleting text on a non-uniform background confirm that the information is completely deleted without affecting the rest image areas.

Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. Key points: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations. [ABSTRACT FROM AUTHOR]

Classical magnetic fields might change the properties of topological insulators such as the time reversal symmetry protected topological edge states. This poses a question that whether quantized fields would change differently the feature of topological materials with respect to the classical one. In this paper, we propose a model to describe topological insulators (ultracold atoms in square optical lattices with magnetic field) coupled to a tunable single-mode quantized field, and discuss the topological features of the system. We find that the quantized field can induce topological quantum phase transitions in a different way. To be specific, for fixed gauge magnetic flux ratio, we calculate the energy bands for different coupling constants between the systems and the fields in both open and periodic boundary conditions. We find that the Hofstadter butterfly graph is divided into a pair for continuous gauge magnetic flux ratio, which is different from the one without single-mode quantized field. In addition, we plot topological phase diagrams characterized by Chern number as a function of the momentum of the single-mode quantized field and obtain a quantized structure with non-zero filling factor. [ABSTRACT FROM AUTHOR]

It has been claimed that Protein-Protein Interaction (PPI) networks are scale free that contain a few hubs with ability to bind multiple proteins. Hubs are classified as party and date hubs. Party hubs generally bind different proteins in specific module simultaneously, while date hubs interact with multiple proteins in different modules at different times and locations. Generally, they have been divided into two classes based on the average Pear- son Correlation Coefficient (avPCC) of expression over all partners or their functions. In this study, we propose a two-step algorithm to classify party and date hubs based on their topological features of PPI network. In the first step, we calculate some topological features for each hub vertex in PPI network. In the second step, we apply an unsupervised learning model to calculate Laplacian score for each feature. The Laplace value for each hub vertex are considered based on Laplacian scores. Finally, the hub vertices are classified into two classes date hubs and party hubs with respect to Laplace values. We evaluate our method on reference hubs based on the avPCC on PPI network. We show that the combination of topological features based on ULPD can improve the performance of each topological feature. Finally, we investigate the performance of our method for human dataset and analyze two types of hubs as drug targets for Covid-19.

Background: Corneal fluorescein staining is a key biomarker in evaluating dry eye disease. However, subjective scales of corneal fluorescein staining are lacking in consistency and increase the difficulties of an accurate diagnosis for clinicians. This study aimed to propose an automatic machine learning-based method for corneal fluorescein staining evaluation by utilizing prior information about the spatial connection and distribution of the staining region. Methods: We proposed an end-to-end automatic machine learning-based classification model that consists of staining region identification, feature signature construction, and machine learning-based classification, which fully scrutinizes the multiscale topological features together with conventional texture and morphological features. The proposed model was evaluated using retrospective data from Beijing Tongren Hospital. Two masked ophthalmologists scored images independently using the Sjögren’s International Collaborative Clinical Alliance Ocular Staining Score scale. Results: A total of 382 images were enrolled in the study. A signature with six topological features, two textural features, and two morphological features was constructed after feature extraction and selection. Support vector machines showed the best classification performance (accuracy: 82.67%, area under the curve: 96.59%) with the designed signature. Meanwhile, topological features contributed more to the classification, compared with other features. According to the distribution and correlation with features and scores, topological features performed better than others. Conclusions: An automatic machine learning-based method was advanced for corneal fluorescein staining evaluation. The topological features in presenting the spatial connectivity and distribution of staining regions are essential for an efficient corneal fluorescein staining evaluation. This result implies the clinical application of topological features in dry-eye diagnosis and therapeutic effect evaluation.

Forest and grass ecological space is the key component of the ecosystem and plays a vital role in regulating the carbon, water, and energy cycle. The long-term exploitation of forest and grass ecological space and huge population pressure have gradually degraded the function of China's ecosystem. Therefore, forest and grass ecological space plays an important role in maintaining the stability of the ecosystem. The relationship between forest and grass ecospatial network structure and ecosystem service has been the focus of research. In this study, the forest and grass ecospatial network is constructed based on the minimum cumulative resistance (MCR) model. Then, the topological indicators (degree, weight clustering coefficient, node weight, unit weight, weight distribution difference, betweenness, PageRank) of the forest and grass ecospatial network were calculated by combining the complex network theory to analyze the relationship between these topological indicators and the three ecosystems (water retention, soil conservation, carbon storage). Based on the ecological significance of topological indicators, we identified ecologically fragile areas and proposed areas and directions for optimizing the ecospatial structure. Results show that the spatial distribution of the three ecosystem services in the southeast region of China is higher than that in the northwest region of China and shows a gradual decrease from the east to the west. The degree, node weight, unit weight, PageRank, and betweenness were highly significant and positively correlated with the three ecosystem services, among which PageRank had the highest correlation with water retention (p < 0.01, R2 = 0.835). Based on the spatial distribution characteristics of the different topological indicators, the quantitative relationship between the structural characteristics of the forest and grass ecospatial network and ecosystem services is clarified, revealing the intrinsic connection between ecological processes and ecosystem services. Through rational optimization of the forest and grass ecospatial network, ecosystem services can be effectively improved and ecosystem stability can be enhanced. [ABSTRACT FROM AUTHOR]

Graph neural networks (GNNs) can deal with complex network structures and model complex syntax structures in natural languages, which makes GNN outstanding in text classification tasks. However, most graph neural network approaches don't seem to take full advantage of the topological gains from document graphs. In this paper, we propose a topologically enhanced text classification method to make full use of the structural features of corpus graph and sentence graph. Specifically, we construct two different graphs based on contextual information, called sentence graphs and corpus graphs, respectively. We extract the topological features of words from the corpus graph and inject them into the graph neural network model based on sentence graph classification. To better integrate the topological features, we propose an asynchronous weighted propagation scheme, which selectively fuses the topological features with the original features of the word nodes, and integrate document features to predict final results. A large number of experiments on eight datasets demonstrate the effectiveness of our method. [ABSTRACT FROM AUTHOR]

Corneal Fluorescence Staining (CFS) imaging is commonly employed for assessing corneal epithelial damage. Automating the grading of CFS images can minimize subjectivity in clinical evaluations and enhance diagnostic efficiency. Existing methods typically depend on the texture and morphological information extracted from whole CFS images, often neglecting the spatial and distribution information between stained regions. This oversight hinders the accurate evaluation of corneal epithelial injury states. This study proposes a three-stage automatic corneal epithelial damage assessment model for full CFS images, optimizing grading by considering topological features among detected stained regions, which are crucial for accurately interpreting the spatial properties of objects within an image. Accurate corneal localization, robust to variations in contrast, is first achieved by integrating CFS images' intensity and phase information, subsequently by a multi-scale morphological top-hat operator concerning their prior shape to detect the stained regions. Finally, a multi-scale graph structure is constructed based on the detected stained areas, and distance-weighted topological features, along with textural and morphological features, are extracted into an automatic grading model based on an ensemble model. Experiments on an in-house dataset of CFS images annotated with six categories of Ocular Surface Staining (OSS) scores reveal that incorporating topological features achieves the highest Accuracy (0.7589), F1 score (0.7449), and AUC (0.9335). Moreover, topological features outperformed other individual features. These findings underscore the effectiveness of our proposed model in CFS grading, indicating its potential for assessing corneal epithelial damage. Additionally, the valuable insights provided by topological features into the spatial distribution patterns of staining suggest promising applications for enhancing disease classification and supporting more informed clinical decision-making in managing dry eye conditions., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Ltd. All rights reserved.)

Persistence landscapes, a sophisticated tool from topological data analysis, offer a promising approach to address biases in radiological interpretation and AI model development. By transforming complex topological features into statistically analyzable functions, they enable robust comparisons between populations and datasets. Persistence landscapes excel in noise filtration, fusion bias mitigation, and enhancing machine learning models. Despite challenges in computation and integration, they show potential to improve the accuracy and equity of radiological analysis, particularly in multi-modal imaging and AI-assisted interpretation.

Abstract Background The study of protein complexes and protein functional modules has become an important method to further understand the mechanism and organization of life activities. The clustering algorithms used to analyze the information contained in protein-protein interaction network are effective ways to explore the characteristics of protein functional modules. Results This paper conducts an intensive study on the problems of low recognition efficiency and noise in the overlapping structure of protein functional modules, based on topological characteristics of PPI network. Developing a protein function module recognition method ECTG based on Topological Features and Gene expression data for Protein Complex Identification. Conclusions The algorithm can effectively remove the noise data reflected by calculating the topological structure characteristic values in the PPI network through the similarity of gene expression patterns, and also properly use the information hidden in the gene expression data. The experimental results show that the ECTG algorithm can detect protein functional modules better.

Summary: Social network analysis (SNA) has attracted a lot of attention in several domains in the past decades. It can be of 2‐folds: one is content‐based, and another one is structured‐based analysis. Link prediction is one of the emerging research problems, which comes under structured‐based analysis that deals with predicting the missing link, which is likely to appear in the future. In this article, the supervised machine learning techniques have been implemented to predict the possibilities of establishing the links in future. The major contribution in this article lies in feature construction from the topological structure of the network. Several structured‐based similarity measures have been considered for preparing the feature vector for each nonexisting links in the network. The performance of the proposed algorithm has been extensively validated by comparing with other link prediction algorithms using both real‐world and synthetic data sets. [ABSTRACT FROM AUTHOR]

Radiomics is a procedure to access quantitative features from medical images for predictive analysis. Radiomics is used extensively for malignancy and survival analysis, genomic expression analysis, cancer progression, and assessment. But radiomics does not obtain the connected components, loops, or voids information from a region of interest. Topological data analysis is a newer approach that uses persistent homology to generate multiscale features from an image. We investigated in this study whether the topological features can be as useful as the radiomics features. Glioma grading and 1p19q codeletion assessment requires surgical biopsy, which can be error prone. To reduce biopsy error, MRI‐based radiomics and topological features–based analysis were performed in our study. Topological features produced the best results for 1p19q status and tumor‐grade prediction, with 94.3% (0.93 AUC) and 97.3% (0.97 AUC), respectively, which was an improvement over radiomics. Codes and partial data are available in https://github.com/hellorp1990/TDA-analysis. [ABSTRACT FROM AUTHOR]

Being able to capture the characteristics of a time series with a feature vector is a very important task with a multitude of applications, such as classification, clustering or forecasting. Usually, the features are obtained from linear and nonlinear time series measures, that may present several data related drawbacks. In this work we introduce NetF as an alternative set of features, incorporating several representative topological measures of different complex networks mappings of the time series. Our approach does not require data preprocessing and is applicable regardless of any data characteristics. Exploring our novel feature vector, we are able to connect mapped network features to properties inherent in diversified time series models, showing that NetF can be useful to characterize time data. Furthermore, we also demonstrate the applicability of our methodology in clustering synthetic and benchmark time series sets, comparing its performance with more conventional features, showcasing how NetF can achieve high-accuracy clusters. Our results are very promising, with network features from different mapping methods capturing different properties of the time series, adding a different and rich feature set to the literature. [ABSTRACT FROM AUTHOR]

User relations and information propagation on social networks can reflect events in real society. Online detection of bursty events is of great significance to studying the evolution of social networks and cyberspace security. Current research works focus on building an event recognition model based on text information and then utilizing clustering or topic model methods to extract features from the data stream and then detect events that have not existed before. The text-based method is designed for specific content, and it does not consider the features of network dynamic evolution. It is restricted by the type and quality of text in social networks, limiting its practical application scenarios. However, there exist remarkable correlations between the occurrence of events and the evolution of the network. In this paper, we consider mining the network structure changes to identify bursty events, the superiority which is that it is sensitive and widely used. We integrate snapshot network topology indexes to quantify its structural features. Then we can judge whether there is a burst event by investigating the change degree of the network structure features of the adjacent snapshots. The effectiveness and efficiency of our approach are further confirmed by experimental studies on four real social network data sets. In addition, we also discuss the salient features of the bursty events and compare the impact of the bursty events on the network structure with that of the scheduled events. [ABSTRACT FROM AUTHOR]

Skull prediction from the head is a challenging issue toward a cost-effective therapeutic solution for facial disorders. This issue was initially studied in our previous work using full head-to-skull relationship learning. However, the head-skull thickness topology is locally shaped, especially in the face region. Thus, the objective of the present study was to enhance our head-to-skull prediction problem by using local topological features for training and predicting. Head and skull feature points were sampled on 329 head and skull models from computed tomography (CT) images. These feature points were classified into the back and facial topologies. Head-to-skull relations were trained using the partial least square regression (PLSR) models separately in the two topologies. A hyperparameter tuning process was also conducted for selecting optimal parameters for each training model. Thus, a new skull could be generated so that its shape was statistically fitted with the target head. Mean errors of the predicted skulls using the topology-based learning method were better than those using the non-topology-based learning method. After tenfold cross-validation, the mean error was enhanced 36.96% for the skull shapes and 14.17% for the skull models. Mean error in the facial skull region was especially improved with 4.98%. The mean errors were also improved 11.71% and 25.74% in the muscle attachment regions and the back skull regions respectively. Moreover, using the enhanced learning strategy, the errors (mean ± SD) for the best and worst prediction cases are from 1.1994 ± 1.1225 mm (median: 0.9036, coefficient of multiple determination (R2): 0.997274) to 3.6972 ± 2.4118 mm (median: 3.9089, R2: 0.999614) and from 2.0172 ± 2.0454 mm (median: 1.2999, R2: 0.995959) to 4.0227 ± 2.6098 mm (median: 3.9998, R2: 0.998577) for the predicted skull shapes and the predicted skull models respectively. This present study showed that more detailed information on the head-skull shape leads to a better accuracy level for the skull prediction from the head. In particular, local topological features on the back and face regions of interest should be considered toward a better learning strategy for the head-to-skull prediction problem. In perspective, this enhanced learning strategy was used to update our developed clinical decision support system for facial disorders. Furthermore, a new class of learning methods, called geometric deep learning will be studied. [ABSTRACT FROM AUTHOR]

To recognize the basis of disease, it is essential to determine its underlying genes. Understanding the association between underlying genes and genetic disease is a fundamental problem regarding human health. Identification and association of genes with the disease require time consuming and expensive experimentations of a great number of potential candidate genes. Therefore, the alternative inexpensive and rapid computational methods have been proposed that can identify the candidate gene associated with a disease. Most of these methods use phenotypic similarities due to the fact that genes causing same or similar diseases have less variation in their sequence or network properties of protein-protein interactions based on-premises that genes lie closer in protein interaction network that causes the similar or same disease. However, these methods use only basic network properties or topological features and gene sequence information or biological features as a prior knowledge for identification of gene-disease association, which restricts the identification process to a single gene-disease association. In this study, we propose and analyze some novel computational methods for the identification of genes associated with diseases. Some advance topological and biological features that are overlooked currently are introducing for identifying candidate genes. We evaluate different computational methods on disease-gene association data from DisGeNET in a 10-fold cross-validation mode based on TP rate, FP rate, precision, recall, F-measure, and ROC curve evaluation parameters. The results reveal that various computational methods with advanced feature set outperform previous state-of-the-art techniques by achieving precision up to 93.8%, recall up to 93.1%, and F- measure up to 92.9%. Significantly, we apply our methods to study four major diseases: Thalassemia, Diabetes, Malaria, and Asthma. Simulation results show that the proposed Deep Extreme Learning Machine (DELM) gives more accurate results as compared to previously published approaches.

Physical quality assessment of harvested soybeans is one of the basic requirements in the commercial trade market. The image-processing-based automated system helps to achieve reliability in quality assessment over the manual inspection method. Image acquisition and object detection are the crucial blocks of such automated systems. In this paper, we propose an improved image acquisition system to acquire two-sided images of harvested soybean samples. During the object detection process, the watershed algorithm is commonly used to separate connected objects. However, the performance of the watershed algorithm degrades for harvested soybeans due to the loss of object information. We propose a linear staircase path approximation scheme (LSPA) to disconnect objects with higher accuracy. The LSPA scheme utilizes the topological features of connected objects, which is less sensitive to the local variation of object features. The LSPA scheme identifies the objects of harvested soybean samples with marginal variation in object count w.r.t the actual object count, which improves the object classification accuracy. The multi-class and binary classification jointly performed to improve the classification accuracy of sound quality soybean. Experimental results show that the detection accuracy of sound quality soybean is almost 90% for the proposed scheme, which is substantially higher than the existing scheme based on the watershed algorithm. [ABSTRACT FROM AUTHOR]

In this paper, we study the synchronizability of three kinds of dynamical weighted fractal networks (WFNs). These WFNs are weighted Cantor-dust networks, weighted Sierpinski networks and weighted Koch networks. We calculated some features of these WFNs, including average distance ( d avg ), fractal dimension (D (0)), information dimension (D (1)), correlation dimension (D (2)). We analyze two representative types of synchronizable dynamical networks (the type-I and the type-II). There are two indexes ( λ 2  and λ N / λ 2 ) that can be used to characterize the synchronizability of the two types of dynamical network. Here, λ 2 and λ N are the minimum nonzero eigenvalue and the maximum eigenvalue of the Laplacian matrix of the network, respectively. We find that the larger scaling factor f , D (0) , D (1) , D (2) or d avg implies stronger synchronizability for the type-I dynamical WFNs. [ABSTRACT FROM AUTHOR]

Stick-slip vibration images of water-lubricated rubber stern bearing are collected by using machine vision technology. Then these images are analyzed by the methods of persistent homology-based machine learning (PHML). During this analysis, the corresponding barcode is obtained by calculating the homology of the simplicial complex of the vibration images, and the topological characteristics of the vibration images are obtained based on the barcode images, then the support vector machine (SVM) learning is used to study the topological features, and finally the classification and identification of the stick-slip vibration of water-lubricated rubber stern tube bearing are completed. The results have shown that the length of the longest 1D Betti number is closely related to vibration value. Based on these data, it is possible to use the warning beep effectively, create an intelligent description of the beep process, and provide a new idea for simulating stick-slip vibration in the stern bearing. [ABSTRACT FROM AUTHOR]

Forest and grass ecological space is the key component of the ecosystem and plays a vital role in regulating the carbon, water, and energy cycle. The long-term exploitation of forest and grass ecological space and huge population pressure have gradually degraded the function of China’s ecosystem. Therefore, forest and grass ecological space plays an important role in maintaining the stability of the ecosystem. The relationship between forest and grass ecospatial network structure and ecosystem service has been the focus of research. In this study, the forest and grass ecospatial network is constructed based on the minimum cumulative resistance (MCR) model. Then, the topological indicators (degree, weight clustering coefficient, node weight, unit weight, weight distribution difference, betweenness, PageRank) of the forest and grass ecospatial network were calculated by combining the complex network theory to analyze the relationship between these topological indicators and the three ecosystems (water retention, soil conservation, carbon storage). Based on the ecological significance of topological indicators, we identified ecologically fragile areas and proposed areas and directions for optimizing the ecospatial structure. Results show that the spatial distribution of the three ecosystem services in the southeast region of China is higher than that in the northwest region of China and shows a gradual decrease from the east to the west. The degree, node weight, unit weight, PageRank, and betweenness were highly significant and positively correlated with the three ecosystem services, among which PageRank had the highest correlation with water retention (p < 0.01, R2 = 0.835). Based on the spatial distribution characteristics of the different topological indicators, the quantitative relationship between the structural characteristics of the forest and grass ecospatial network and ecosystem services is clarified, revealing the intrinsic connection between ecological processes and ecosystem services. Through rational optimization of the forest and grass ecospatial network, ecosystem services can be effectively improved and ecosystem stability can be enhanced.