scGIR: deciphering cellular heterogeneity via gene ranking in single-cell weighted gene correlation networks.

Single-cell RNA sequencing (scRNA-seq) has emerged as a powerful tool for investigating cellular heterogeneity through high-throughput analysis of individual cells. Nevertheless, challenges arise from prevalent sequencing dropout events and noise effects, impacting subsequent analyses. Here, we introduce a novel algorithm, Single-cell Gene Importance Ranking (scGIR), which utilizes a single-cell gene correlation network to evaluate gene importance. The algorithm transforms single-cell sequencing data into a robust gene correlation network through statistical independence, with correlation edges weighted by gene expression levels. We then constructed a random walk model on the resulting weighted gene correlation network to rank the importance of genes. Our analysis of gene importance using PageRank algorithm across nine authentic scRNA-seq datasets indicates that scGIR can effectively surmount technical noise, enabling the identification of cell types and inference of developmental trajectories. We demonstrated that the edges of gene correlation, weighted by expression, play a critical role in enhancing the algorithm's performance. Our findings emphasize that scGIR outperforms in enhancing the clustering of cell subtypes, reverse identifying differentially expressed marker genes, and uncovering genes with potential differential importance. Overall, we proposed a promising method capable of extracting more information from single-cell RNA sequencing datasets, potentially shedding new lights on cellular processes and disease mechanisms.

Primary driving factors of ecological environment system change based on directed weighted network illustrating with the Three-River Headwaters Region.

The primary driving factors of ecological environment change have received significant attention. However, previous research methods for identifying the main drivers of ecological environment change have primarily relied on correlation analysis and regression analysis. While these methods can reveal co-occurrences, associations, and correlations among elemental characteristics, they often struggle to uncover the deep-seated interactions among elements within complex, unstable, nonlinear, and high-dimensional systems. To address this, we used the Three-River Headwaters Region as a case study and introduced a complex network model from the perspective of the ecological environment system to investigate the main driving factors of ecological environment change. In our analysis, we considered 12 factors related to the atmosphere, hydrology, vegetation, and soil, including evaporation, long-wave radiation, short-wave radiation, specific humidity, soil temperature, precipitation rate, soil water content, air temperature, air pressure, vegetation normalization index, wind speed, and natural surface runoff. Watersheds were selected as the fundamental units for constructing ecological environment datasets. We applied the Ensemble Empirical Mode Decomposition (EEMD) method and Hilbert-Huang Transform (HHT) to analyze causal relationships between time series pairs and constructed two directed weighted network models based on sub-catchments. The results showed that both network models yielded consistent conclusions, with the sparse network exhibiting higher efficiency. Radiation and temperature were identified as the primary driving factors of ecosystem change, and the water cycle was determined to be the ultimate manifestation of ecological system change throughout the Three-River Headwaters Region. Furthermore, based on node out-strength, we generated a vegetation protection priority map.

Identification of a novel gene signature for the prognosis of sepsis.

Sepsis is a life-threatening organ dysfunction caused by the host's dysfunctional response to infection, and its pathogenesis is still unclear. In view of the complex pathological process of sepsis, finding suitable biomarkers is helpful for the research and treatment of sepsis. This study determined the potential prognostic markers of sepsis by analyzing the molecular characteristics of patients with sepsis. During this study, bioinformatics analysis was conducted on the RNA sequencing data and DNA methylation sites from the public database to determine the prognostic genes related to sepsis, and a 9-gene prognostic signature for sepsis was constructed. According to the risk score, all sepsis samples were divided into two groups. Then, the prediction effect of the 9-gene signature was verified in two cohorts, and the association between these genes and sepsis was further revealed through immune infiltration analysis, gene set enrichment analysis and the relationship between clinical phenotype and survival rate. Our study provided a reliable prognostic signature for sepsis. The signature could predict the survival of patients with sepsis and serve as a predictor.

Convolutional Neural Network Bootstrapped by Dynamic Segmentation and Stigmergy-Based Encoding for Real-Time Human Activity Recognition in Smart Homes.

Recently, deep learning (DL) approaches have been extensively employed to recognize human activities in smart buildings, which greatly broaden the scope of applications in this field. Convolutional neural networks (CNN), well known for feature extraction and activity classification, have been applied for estimating human activities. However, most CNN-based techniques usually focus on divided sequences associated to activities, since many real-world employments require information about human activities in real time. In this work, an online human activity recognition (HAR) framework on streaming sensor is proposed. The methodology incorporates real-time dynamic segmentation, stigmergy-based encoding, and classification with a CNN2D. Dynamic segmentation decides if two succeeding events belong to the same activity segment or not. Then, because a CNN2D requires a multi-dimensional format in input, stigmergic track encoding is adopted to build encoded features in a multi-dimensional format. It adopts the directed weighted network (DWN) that takes into account the human spatio-temporal tracks with a requirement of overlapping activities. It represents a matrix that describes an activity segment. Once the DWN for each activity segment is determined, a CNN2D with a DWN in input is adopted to classify activities. The proposed approach is applied to a real case study: the "Aruba" dataset from the CASAS database.

A Protein Co-Conservation Network Model Characterizes Mutation Effects on SARS-CoV-2 Spike Protein.

The emergence of numerous variants of SARS-CoV-2 has presented challenges to the global efforts to control the COVID-19 pandemic. The major mutation is in the SARS-CoV-2 viral envelope spike protein that is responsible for virus attachment to the host, and is the main target for host antibodies. It is critically important to study the biological effects of the mutations to understand the mechanisms of how mutations alter viral functions. Here, we propose a protein co-conservation weighted network (PCCN) model only based on the protein sequence to characterize the mutation sites by topological features and to investigate the mutation effects on the spike protein from a network view. Frist, we found that the mutation sites on the spike protein had significantly larger centrality than the non-mutation sites. Second, the stability changes and binding free energy changes in the mutation sites were positively significantly correlated with their neighbors' degree and the shortest path length separately. The results indicate that our PCCN model provides new insights into mutations on spike proteins and reflects the mutation effects on protein function alternations.

Robustness of Multi-Project Knowledge Collaboration Network in Open Source Community.

Multi-project parallelism is an important feature of open source communities (OSCs), and multi-project collaboration among users is a favorable condition for an OSC's development. This paper studies the robustness of this type of community. Based on the characteristics of knowledge collaboration behavior and the large amount of semantic content generated from user collaboration in open source projects, we construct a directed, weighted, semantic-based multi-project knowledge collaboration network. Using analysis of the KCN's structure and user attributes, nodes are divided into knowledge collaboration nodes and knowledge dissemination nodes that participate in either multi- or single-project collaboration. From the perspectives of user churn and behavior degradation, two types of failure modes are constructed: node failure and edge failure. Based on empirical data from the Local Motors open source vehicle design community, we then carry out a dynamic robustness analysis experiment. Our results show that the robustness of our constructed network varies for different failure modes and different node types: the network has (1) a high robustness to random failure and a low robustness to deliberate failure, (2) a high robustness to edge failure and a low robustness to node failure, and (3) a high robustness to the failure of single-project nodes (or their edges) and a low robustness to the failure of multi-project nodes (or their edges). These findings can be used to provide a more comprehensive and targeted management reference, promoting the efficient development of OSCs.

Category weighted network and relation weighted label for diabetic retinopathy screening.

Diabetic retinopathy (DR) is the primary cause of blindness in adults. Incorporating machine learning into DR grading can improve the accuracy of medical diagnosis. However, problems, such as severe data imbalance, persists. Existing studies on DR grading ignore the correlation between its labels. In this study, a category weighted network (CWN) was proposed to achieve data balance at the model level. In the CWN, a reference for weight settings is provided by calculating the category gradient norm and reducing the experimental overhead. We proposed to use relation weighted labels instead of the one-hot label to investigate the distance relationship between labels. Experiments revealed that the proposed CWN achieved excellent performance on various DR datasets. Furthermore, relation weighted labels exhibit broad applicability and can improve other methods using one-hot labels. The proposed method achieved kappa scores of 0.9431 and 0.9226 and accuracy of 90.94% and 86.12% on DDR and APTOS datasets, respectively.

An effective distance-based centrality approach for exploring the centrality of maritime shipping network.

Centrality has always been used in transportation networks to estimate the status and importance of a node in the networks, especially in the shipping networks. However, most of the studies only take the shipping network as an unweighted network or only considering the tie weights in the weighted networks, ignoring the truth that both the number of ties and tie weights contribute to the centrality in weighted shipping networks. Therefore, we proposed a new method combining both the number of ties and tie weights to assess the node centrality based on effective distance by integrating the studies of Opsahl et al., (2010) and Du et al., (2015). An empirical analysis of shipping network at the country level for the 21st-centrtury Maritime Silk Road (MSR) was performed. The result of correlation analysis between country's degree centrality and the Liner Shipping Connectivity Index (LSCI) published by the United Nations Conference on Trade and Development (UNCTAD) proved the superiority of our method compared to the traditional centrality metrics. In weighted networks, both the number of ties the tie weights should be considered by adjusting the parameters. The method proposed in this study can also be used to nodes' status and importance estimation of various networks in other fields.

Research on Computer-Aided Diagnosis Method Based on Symptom Filtering and Weighted Network.

In the process of disease identification, as the number of diseases increases, the collection of both diseases and symptoms becomes larger. However, existing computer-aided diagnosis systems do not completely solve the dimensional disaster caused by the increasing data set. To address the above problems, we propose methods of using symptom filtering and a weighted network with the goal of deeper processing of the collected symptom information. Symptom filtering is similar to a filter in signal transmission, which can filter the collected symptom information, further reduce the dimensional space of the system, and make the important symptoms more prominent. The weighted network, on the other hand, mines deeper disease information by modeling the channels of symptom information, amplifying important information, and suppressing unimportant information. Compared with existing hierarchical reinforcement learning models, the feature extraction methods proposed in this paper can help existing models improve their accuracy by more than 10%.

A New Way to Trace SARS-CoV-2 Variants Through Weighted Network Analysis of Frequency Trajectories of Mutations.

Early detection of SARS-CoV-2 variants enables timely tracking of clinically important strains in order to inform the public health response. Current subtype-based variant surveillance depending on prior subtype assignment according to lag features and their continuous risk assessment may delay this process. We proposed a weighted network framework to model the frequency trajectories of mutations (FTMs) for SARS-CoV-2 variant tracing, without requiring prior subtype assignment. This framework modularizes the FTMs and conglomerates synchronous FTMs together to represent the variants. It also generates module clusters to unveil the epidemic stages and their contemporaneous variants. Eventually, the module-based variants are assessed by phylogenetic tree through sub-sampling to facilitate communication and control of the epidemic. This process was benchmarked using worldwide GISAID data, which not only demonstrated all the methodology features but also showed the module-based variant identification had highly specific and sensitive mapping with the global phylogenetic tree. When applying this process to regional data like India and South Africa for SARS-CoV-2 variant surveillance, the approach clearly elucidated the national dispersal history of the viral variants and their co-circulation pattern, and provided much earlier warning of Beta (B.1.351), Delta (B.1.617.2), and Omicron (B.1.1.529). In summary, our work showed that the weighted network modeling of FTMs enables us to rapidly and easily track down SARS-CoV-2 variants overcoming prior viral subtyping with lag features, accelerating the understanding and surveillance of COVID-19.

Online Activity Recognition Combining Dynamic Segmentation and Emergent Modeling.

Activity recognition is fundamental to many applications envisaged in pervasive computing, especially in smart environments where the resident's data collected from sensors will be mapped to human activities. Previous research usually focuses on scripted or pre-segmented sequences related to activities, whereas many real-world deployments require information about the ongoing activities in real time. In this paper, we propose an online activity recognition model on streaming sensor data that incorporates the spatio-temporal correlation-based dynamic segmentation method and the stigmergy-based emergent modeling method to recognize activities when new sensor events are recorded. The dynamic segmentation approach integrating sensor correlation and time correlation judges whether two consecutive sensor events belong to the same window or not, avoiding events from very different functional areas or with a long time interval in the same window, thus obtaining the segmented window for every single event. Then, the emergent paradigm with marker-based stigmergy is adopted to build activity features that are explicitly represented as a directed weighted network to define the context for the last sensor event in this window, which does not need sophisticated domain knowledge. We validate the proposed method utilizing the real-world dataset Aruba from the CASAS project and the results show the effectiveness.

A network generator for covert network structures.

We focus on organizational structures in covert networks, such as criminal or terrorist networks. Their members engage in illegal activities and attempt to hide their association and interactions with these networks. Hence, data about such networks are incomplete. We introduce a novel method of rewiring covert networks parameterized by the edge connectivity standard deviation. The generated networks are statistically similar to themselves and to the original network. The higher-level organizational structures are modeled as a multi-layer network while the lowest level uses the Stochastic Block Model. Such synthetic networks provide alternative structures for data about the original network. Using them, analysts can find structures that are frequent, therefore stable under perturbations. Another application is to anonymize generated networks and use them for testing new software developed in open research facilities. The results indicate that modeling edge structure and the hierarchy together is essential for generating networks that are statistically similar but not identical to each other or the original network. In experiments, we generate many synthetic networks from two covert networks. Only a few structures of synthetics networks repeat, with the most stable ones shared by 18% of all synthetic networks making them strong candidates for the ground truth structure.

A Latent Space Model for HLA Compatibility Networks in Kidney Transplantation.

Kidney transplantation is the preferred treatment for people suffering from end-stage renal disease. Successful kidney transplants still fail over time, known as graft failure; however, the time to grant failure, or graft survival time, can vary significantly between different recipients. A significant biological factor affecting graft survival times is the compatibility between the human leukocyte antigens (HLAs) of the donor and recipient. We propose to model HLA compatibility using a network, where the nodes denote different HLAs of the donor and recipient, and edge weights denote compatibilities of the HLAs, which can be positive or negative. The network is indirectly observed, as the edge weights are estimated from transplant outcomes rather than directly observed. We propose a latent space model for such indirectly-observed weighted and signed networks. We demonstrate that our latent space model can not only result in more accurate estimates of HLA compatibilities, but can also be incorporated into survival analysis models to improve accuracy for the downstream task of predicting graft survival times.

[An optimization method of weighted network module partition based on TCM theory of "monarch, minister, assistant and guide"].

The disease-gene-drug multi-level network constructed by network pharmacology can predict drug targets and has been widely used in the study of material basis and mechanism of action of Chinese medicinal prescriptions. However, most of the current studies have normalized the efficacies of Chinese herbal medicines in the compounds during the construction of the network. There is also a lack of in-depth exploration of the mechanism of synergy among multiple components. This study proposed a network module partition method based on group collaboration and the pharmacological network was weighed according to the traditional Chinese medicine(TCM) theory of "monarch, minister, assistant and guide". Taking the Tanyu Tongzhi Prescription as an example, we constructed its pharmacological network for the treatment of myocardial ischemia-reperfusion injury. The group collaboration module in the network was identified and the network changes before and after the weighting were compared based on the network topology analysis to explore a new method to find the core nodes of the network as well as the core drugs that affected the efficacy of the compounds. The results showed that the module partition method based on group collaboration could be used to identify and partition group collaboration mo-dules in pharmacological networks of compounds. The proposed weighted network based on the TCM theory of "monarch, minister, assistant, and guide" could identify and partition the modules based on the characteristics of the pharmacological network. The identification and partition results of modules of Tanyu Tongzhi Prescription in the weighted network were superior to those in the unweighted network. The weighted closeness centrality(WCC) evaluation method was conducive to finding key nodes and relations in the network as compared with traditional methods, thereby providing a basis for analyzing the core components of drugs and extracting more accurate drug components and targets.

Entropy and Network Centralities as Intelligent Tools for the Investigation of Terrorist Organizations.

In recent years, law enforcement authorities have increasingly used mathematical tools to support criminal investigations, such as those related to terrorism. In this work, two relevant questions are discussed: "How can the different roles of members of a terrorist organization be recognized?" and "are there early signs of impending terrorist acts?" These questions are addressed using the tools of entropy and network theory, more specifically centralities (degree, betweenness, clustering) and their entropies. These tools were applied to data (physical contacts) of four real terrorist networks from different countries. The different roles of the members are clearly recognized from the values of the selected centralities. An early sign of impending terrorist acts is the evolutionary pattern of the values of the entropies of the selected centralities. These results have been confirmed in all four terrorist networks. The conclusion is expected to be useful to law enforcement authorities to identify the roles of the members of terrorist organizations as the members with high centrality and to anticipate when a terrorist attack is imminent, by observing the evolution of the entropies of the centralities.

A Novel Pathway Network Analytics Method Based on Graph Theory.

A biological pathway is an ordered set of interactions between intracellular molecules having collective activity that impacts cellular function, for example, by controlling metabolite synthesis or by regulating the expression of sets of genes. They play a key role in advanced studies of genomics. However, existing pathway analytics methods are inadequate to extract meaningful biological structure underneath the network of pathways. They also lack automation. Given these circumstances, we have come up with a novel graph theoretic method to analyze disease-related genes through weighted network of biological pathways. The method automatically extracts biological structures, such as clusters of pathways and their relevance, significance of each pathway and gene, and so forth hidden in the complex network. We have demonstrated the effectiveness of the proposed method on a set of genes associated with coronavirus disease 2019.

Survival-Based Biomarker Module Identification Associated with Oral Squamous Cell Carcinoma (OSCC).

Head and neck squamous cell carcinoma (HNSC) is one of the most common malignant tumors worldwide with a high rate of morbidity and mortality, with 90% of predilections occurring for oral squamous cell carcinoma (OSCC). Cancers of the mouth account for 40% of head and neck cancers, including squamous cell carcinomas of the tongue, floor of the mouth, buccal mucosa, lips, hard and soft palate, and gingival. OSCC is the most devastating and commonly occurring oral malignancy, with a mortality rate of 500,000 deaths per year. This has imposed a strong necessity to discover driver genes responsible for its progression and malignancy. In the present study we filtered oral squamous cell carcinoma tissue samples from TCGA-HNSC cohort, which we followed by constructing a weighted PPI network based on the survival of patients and the expression profiles of samples collected from them. We found a total of 46 modules, with 18 modules having more than five edges. The KM and ME analyses revealed a single module (with 12 genes) as significant in the training and test datasets. The genes from this significant module were subjected to pathway enrichment analysis for identification of significant pathways and involved genes. Finally, the overlapping genes between gene sets ranked on the basis of weighted PPI module centralities (i.e., degree and eigenvector), significant pathway genes, and DEGs from a microarray OSCC dataset were considered as OSCC-specific hub genes. These hub genes were clinically validated using the IHC images available from the Human Protein Atlas (HPA) database.

Multimorbidity study with different levels of depression status.

OBJECTIVE: Depression is one of the leading causes of disability burden and frequently co-occurs with multiple chronic diseases, but limited research has yet evaluated the correlation between multimorbidity and depression status by sex and age. METHODS: 29303 adults from 2005-2016 National Health and Nutrition Examination Survey were involved in the study. The validated Patient Health Questionnaire (PHQ-9) was used to assess depression status. The linear trend of the prevalence of multimorbidity was tested by logistic regressions, which was visualized by the weighted network. Gamma coefficient (γ) was used to evaluate the correlation between multimorbidity and depression status. RESULTS: The prevalence of multimorbidity in participants with no depression, mild depression, moderate depression and severe depression was 52.1%, 63.0%, 68.4% and 76.1%, respectively (p for trend < 0.001). In network analysis, the absolute network density increased with the levels of depression status (from 4.54 to 15.04). Positive correlation was identified between multimorbidity and depression status (γ=0.21, p<0.001), and the correlation was different by sex and age, where it was stronger in women than men (females: γ=0.23, males: γ=0.16), and stronger in the young and the middle-age (young: γ=0.30, middle-age: γ=0.29, old: γ=0.22). LIMITATIONS: This is a cross-sectional study and thus we cannot draw firm conclusions on causal correlations. CONCLUSIONS: Positive correlation between multimorbidity and depression status was identified, where the number of multimorbidity increased with the levels of depression status, especially in females, the young and the middle-age.

Dynamic Robustness of Semantic-Based Collaborative Knowledge Network of Open Source Project.

Robustness of the collaborative knowledge network (CKN) is critical to the success of open source projects. To study this robustness more comprehensively and accurately, we constructed a weighted CKN based on the semantic analysis of collaborative behavior, where (a) open source designers were the network nodes, (b) collaborative behavior among designers was the edges, and (c) collaborative text content intensity and collaborative frequency intensity were the edge weights. To study the robustness from a dynamic viewpoint, we constructed three CKNs from different stages of the project life cycle: the start-up, growth and maturation stages. The connectivity and collaboration efficiency of the weighted network were then used as robustness evaluation indexes. Further, we designed four edge failure modes based on the behavioral characteristics of open source designers. Finally, we carried out dynamic robustness analysis experiments based on the empirical data of a Local Motors open source car design project. Our results showed that the CKN performed differently at different stages of the project life cycle, and our specific findings could help community managers of open source projects to formulate different network protection strategies at different stages of their projects.

An optimization method of weighted network module partition based on TCM theory of "monarch, minister, assistant and guide" / 中国中药杂志

The disease-gene-drug multi-level network constructed by network pharmacology can predict drug targets and has been widely used in the study of material basis and mechanism of action of Chinese medicinal prescriptions. However, most of the current studies have normalized the efficacies of Chinese herbal medicines in the compounds during the construction of the network. There is also a lack of in-depth exploration of the mechanism of synergy among multiple components. This study proposed a network module partition method based on group collaboration and the pharmacological network was weighed according to the traditional Chinese medicine(TCM) theory of "monarch, minister, assistant and guide". Taking the Tanyu Tongzhi Prescription as an example, we constructed its pharmacological network for the treatment of myocardial ischemia-reperfusion injury. The group collaboration module in the network was identified and the network changes before and after the weighting were compared based on the network topology analysis to explore a new method to find the core nodes of the network as well as the core drugs that affected the efficacy of the compounds. The results showed that the module partition method based on group collaboration could be used to identify and partition group collaboration mo-dules in pharmacological networks of compounds. The proposed weighted network based on the TCM theory of "monarch, minister, assistant, and guide" could identify and partition the modules based on the characteristics of the pharmacological network. The identification and partition results of modules of Tanyu Tongzhi Prescription in the weighted network were superior to those in the unweighted network. The weighted closeness centrality(WCC) evaluation method was conducive to finding key nodes and relations in the network as compared with traditional methods, thereby providing a basis for analyzing the core components of drugs and extracting more accurate drug components and targets.