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In automata networks, it is well known that the way entities update their states over time has a major impact on their dynamics. In particular, depending on the chosen update schedule, the underlying dynamical systems may exhibit more or less asymptotic dynamical behaviours such as fixed points or limit cycles. Since such mathematical models have been used in the framework of biological networks modelling, the question of choosing appropriate update schedules has arised soon. In this note, focusing on Boolean networks, our aim is to emphasise that the adequate way of thinking regulations and genetic expression over time is certainly not to consider a wall segregating synchronicity from asynchronicity because they actually complement rather well. In particular, we highlight that specific update schedules, namely block-parallel update schedules, whose intrinsic features are still not known from a theoretical point of view, admit realistic and pertinent properties in the context of biological modelling and deserve certainly more attention from the community. [ABSTRACT FROM AUTHOR]

TEX file as is needed for processing, selecting the file designation of TeX/LaTeX Suppl File. Graph Professor Waterman is one of the founders of the field of computational biology and has made many fundamental contributions to the field. [Extracted from the article]

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The University of Texas at Dallas has proposed 24 top journals (UTD24) covering all areas related to management. UTD24 are currently the most authoritative management journals. Institutions or research scholars who have published papers in these journals are considered to have a high academic level. This study uses the paper quality published by an institution in the UTD24 journals to indicate the research quality of this institution and takes the papers published by Chinese Business School in the UTD24 journals from 2000 to 2018 as the research object. By analyzing the staged evolution process and the research hotspot of international research collaboration network (IRC network) of Chinese Business School, this paper summarizes and analyzes the factors that influence the quality of papers published by Chinese Business School in UTD24 journals: degree centrality of an institution, betweenness centrality of an institution, the degree of attention of an institution, the degree of novelty of an institution, and the number of countries cooperating with the institution. This paper divides paper quality into two parts: the total number of papers and citations per paper of an institution. Among them, degree centrality and betweenness centrality of the institution have a significant positive impact on the total number of papers of the institution. The degree of attention and the number of countries cooperating with the institution have a significant positive impact on citations per paper, and the degree of novelty has a significant negative impact on citations per paper. [ABSTRACT FROM AUTHOR]

Motivation The rapid increase of bio-medical literature makes it harder and harder for scientists to keep pace with the discoveries on which they build their studies. Therefore, computational tools have become more widespread, among which network analysis plays a crucial role in several life-science contexts. Nevertheless, building correct and complete networks about some user-defined biomedical topics on top of the available literature is still challenging. Results We introduce NetMe 2.0, a web-based platform that automatically extracts relevant biomedical entities and their relations from a set of input texts—i.e. in the form of full-text or abstract of PubMed Central's papers, free texts, or PDFs uploaded by users—and models them as a BioMedical Knowledge Graph (BKG). NetMe 2.0 also implements an innovative Retrieval Augmented Generation module (Graph-RAG) that works on top of the relationships modeled by the BKG and allows the distilling of well-formed sentences that explain their content. The experimental results show that NetMe 2.0 can infer comprehensive and reliable biological networks with significant Precision–Recall metrics when compared to state-of-the-art approaches. Availability and implementation https://netme.click/. [ABSTRACT FROM AUTHOR]

One of the key problems the brain faces is inferring the state of the world from a sequence of dynamically changing stimuli, and it is not yet clear how the sensory system achieves this task. A well-established computational framework for describing perceptual processes in the brain is provided by the theory of predictive coding. Although the original proposals of predictive coding have discussed temporal prediction, later work developing this theory mostly focused on static stimuli, and key questions on neural implementation and computational properties of temporal predictive coding networks remain open. Here, we address these questions and present a formulation of the temporal predictive coding model that can be naturally implemented in recurrent networks, in which activity dynamics rely only on local inputs to the neurons, and learning only utilises local Hebbian plasticity. Additionally, we show that temporal predictive coding networks can approximate the performance of the Kalman filter in predicting behaviour of linear systems, and behave as a variant of a Kalman filter which does not track its own subjective posterior variance. Importantly, temporal predictive coding networks can achieve similar accuracy as the Kalman filter without performing complex mathematical operations, but just employing simple computations that can be implemented by biological networks. Moreover, when trained with natural dynamic inputs, we found that temporal predictive coding can produce Gabor-like, motion-sensitive receptive fields resembling those observed in real neurons in visual areas. In addition, we demonstrate how the model can be effectively generalized to nonlinear systems. Overall, models presented in this paper show how biologically plausible circuits can predict future stimuli and may guide research on understanding specific neural circuits in brain areas involved in temporal prediction. Author summary: While significant advances have been made in the neuroscience of how the brain processes static stimuli, the time dimension has often been relatively neglected. However, time is crucial since the stimuli perceived by our senses typically dynamically vary in time, and the cortex needs to make sense of these changing inputs. This paper describes a computational model of cortical networks processing temporal stimuli. This model is able to infer and track the state of the environment based on noisy inputs, and predict future sensory stimuli. By ensuring that these predictions match the incoming stimuli, the model is able to learn the structure and statistics of its temporal inputs and produces responses of neurons resembling those in the brain. The model may help in further understanding neural circuits in sensory cortical areas. [ABSTRACT FROM AUTHOR]

In this paper we describe types of evolutions of networks (modelled as graphs) by analyzing the compositions between Hamiltonian graphs and graph "bugs". We identify one type of "superbug": a bug structure that can destroy the Hamiltonicity of a graph (and thus render a potentially-optimal delivery network inefficient), and also describe types of graphbug infections and their effects. [ABSTRACT FROM AUTHOR]

Circular RNA (CircRNA)–microRNA (miRNA) interaction (CMI) is an important model for the regulation of biological processes by non-coding RNA (ncRNA), which provides a new perspective for the study of human complex diseases. However, the existing CMI prediction models mainly rely on the nearest neighbor structure in the biological network, ignoring the molecular network topology, so it is difficult to improve the prediction performance. In this paper, we proposed a new CMI prediction method, BEROLECMI, which uses molecular sequence attributes, molecular self-similarity, and biological network topology to define the specific role feature representation for molecules to infer the new CMI. BEROLECMI effectively makes up for the lack of network topology in the CMI prediction model and achieves the highest prediction performance in three commonly used data sets. In the case study, 14 of the 15 pairs of unknown CMIs were correctly predicted. [ABSTRACT FROM AUTHOR]

Analyzing protein–protein interaction (PPI) networks using machine learning and deep learning algorithms, alongside centrality measures, holds paramount importance in understanding complex biological systems. These advanced computational techniques enable the extraction of valuable insights from intricate network structures, shedding light on the functional relationships between proteins. By leveraging AI-driven approaches, researchers can uncover key regulatory mechanisms, identify critical nodes within the network and predict novel protein interactions with high accuracy. Ultimately, this integration of computational methodologies enhances our ability to comprehend the dynamic behavior of biological systems at a molecular level, paving the way for advancements in drug discovery, disease understanding and personalized medicine. This review paper starts by outlining various popular available PPI network databases and network centrality calculation tools. A thorough classification of various centrality measures has been identified. It primarily delves into the centrality-driven discoveries within PPI networks in biological systems and suggests using edge centrality measures and a hybrid version of node and edge centrality measures in machine learning algorithms and deep learning algorithms to predict hidden knowledge much more effectively. The review paper begins by outlining various popular available PPI network databases and network centrality calculation tools. A thorough classification of various centrality measures has been identified. A detailed view of various findings of different types of centrality measures in PPI networks is presented. [ABSTRACT FROM AUTHOR]

The article presents a response from the authors of the article "Proper evaluation of alignment-free network comparison methods" to a letter to the editor published in the previous issue criticizing the article.

Background: In bioinformatics, interactions are modelled as networks, based on graph models. Generally, these support a single-layer structure which incorporates a specific entity (i.e., node) and only one type of link (i.e., edge). However, real-world biological systems consisting of biological objects belonging to heterogeneous entities, and these operate and influence each other in multiple contexts, simultaneously. Usually, node similarities are investigated to assess the relatedness between biological objects in a network of interest, and node embeddings are widely used for studying novel interaction from a topological point of view. About that, the state-of-the-art presents several methods for evaluating the node similarity inside a given network, but methodologies able to evaluate similarities between pairs of nodes belonging to different networks are missing. The latter are crucial for studies that relate different biological networks, e.g., for Network Alignment or to evaluate the possible evolution of the interactions of a little-known network on the basis of a well-known one. Existing methods are ineffective in evaluating nodes outside their structure, even more so in the context of multilayer networks, in which the topic still exploits approaches adapted from static networks. In this paper, we presented pyMulSim, a novel method for computing the pairwise similarities between nodes belonging to different multilayer networks. It uses a Graph Isomorphism Network (GIN) for the representative learning of node features, that uses for processing the embeddings and computing the similarities between the pairs of nodes of different multilayer networks. Results: Our experimentation investigated the performance of our method. Results show that our method effectively evaluates the similarities between the biological objects of a source multilayer network to a target one, based on the analysis of the node embeddings. Results have been also assessed for different noise levels, also through statistical significance analyses properly performed for this purpose. Conclusions: PyMulSim is a novel method for computing the pairwise similarities between nodes belonging to different multilayer networks, by using a GIN for learning node embeddings. It has been evaluated both in terms of performance and validity, reporting a high degree of reliability. [ABSTRACT FROM AUTHOR]

Community detection is a well-known area of research that yields essential results in various fields such as social media, biological networks, pandemic spread, recommendation systems, etc. There are two important areas for improvement in existing community detection algorithms: quality of community formed should be improved and a parallel approach to community detection is needed to handle massive data. In this paper, we have proposed a three-step parallel algorithm, Par-Com, using the concept of k Clique and modularity optimization to address both of the above issues. The proposed algorithm increases the execution speed and also improves the quality of the community formed by optimizing modularity. Par-Com uses dynamic load balancing on the multicore architecture of Supercomputer ParamShivay. We have also evaluated Par-Com's performance against nine sequential and three parallel community detection algorithms on varying size datasets, i.e. karate, macaque, email, immuno, soc-epinions, facebook, and com-Friendster. The experiment result shows that Par-Com outperforms other algorithms under consideration with up to 45% increase in modularity and up to 84% increase in execution speed. Par-Com is also capable of detecting overlapping communities, fuzzy membership of each node, most influential node in each community formed, and outlier nodes. Nodes within a community that have the highest influence are deemed as experts. The choices made by an expert in a particular community are served as recommendations to other users within that community. [ABSTRACT FROM AUTHOR]

To facilitate the development of large-scale transcriptional regulatory networks (TRNs) that may enable in-silico analyses of disease mechanisms, a reliable catalogue of experimentally verified direct transcriptional regulatory interactions (DTRIs) is needed for training and validation. There has been a long history of using low-throughput experiments to validate single DTRIs. Therefore, we reason that a reliable set of DTRIs could be produced by curating the published literature for such evidence. In our survey of previous curation efforts, we identified the lack of details about the quantity and the types of experimental evidence to be a major gap, despite the theoretical importance of such details for the identification of bona fide DTRIs. We developed a curation protocol to inspect the published literature for support of DTRIs at the experiment level, focusing on genes important to the development of the mammalian nervous system. We sought to record three types of low-throughput experiments: Transcription factor (TF) perturbation, TF-DNA binding, and TF-reporter assays. Using this protocol, we examined a total of 1,310 papers to assemble a collection of 1,499 unique DTRIs, involving 251 TFs and 825 target genes, many of which were not reported in any other DTRI resource. The majority of DTRIs (965; 64%) were supported by two or more types of experimental evidence and 27% were supported by all three. Of the DTRIs with all three types of evidence, 170 had been tested using primary tissues or cells and 44 had been tested directly in the central nervous system. We used our resource to document research biases among reports towards a small number of well-studied TFs. To demonstrate a use case for this resource, we compared our curation to a previously published high-throughput perturbation screen and found significant enrichment of the curated targets among genes differentially expressed in the developing brain in response to Pax6 deletion. This study demonstrates a proof-of-concept for the assembly of a high resolution DTRI resource to support the development of large-scale TRNs. Author summary: The capacity to computationally reconstruct gene regulatory networks using large-scale biological data is currently limited by the absence of a high confidence set of one-to-one regulatory interactions. Given the lengthy history of using small scale experimental assays to investigate individual interactions, we reason that a reliable collection of gene regulatory interactions could be compiled by systematically inspecting the published literature. To this end, we developed a curation protocol to examine and record evidence of regulatory interactions at the individual experiment level. Focusing on the area of brain development, we applied our pipeline to 1,310 publications. We identified 3,601 individual experiments, providing detailed information about 1,499 regulatory interactions. Many of these interactions have verified activity specifically in the embryonic brain. By capturing reports of regulatory interactions at this level of detail, we equip the users with more granular information than other similar resources, enabling more informed assessments of reliability. [ABSTRACT FROM AUTHOR]

In this paper, based on the feedback mechanism from the perspective of network groups, the evolutionary characteristics and laws of group networks under information dissemination are studied. First, the network is divided into groups of different sizes, and each group is given a dynamically changing group activity and a positive degree of response to different categories of information. Second, a feedback-based model of information dissemination in group networks is developed, which takes into account the differences between same-group and cross-group dissemination of information. Next, the model is applied to a scale-free network and a small-world network for simulation experiments. The experimental results show that, under the feedback mechanism, the main factor affecting the final evolutionary results of each group size in the small-world network is group positivity, which has little relationship with the initial size; similarly, the main factor affecting the average degree of each group in the scale-free network is also group positivity, which has nothing to do with the initial average degree. Finally, the method is applied to a real network to verify the rationality and effectiveness of the proposed model. [ABSTRACT FROM AUTHOR]

The potential role of bottom-up Synthetic Cells (SCs) in the Internet of Bio-Nano Things (IoBNT) is discussed. In particular, this perspective paper focuses on the growing interest in networks of biological and/or artificial objects at the micro- and nanoscale (cells and subcellular parts, microelectrodes, microvessels, etc.), whereby communication takes place in an unconventional manner, i.e., via chemical signaling. The resulting "molecular communication" (MC) scenario paves the way to the development of innovative technologies that have the potential to impact biotechnology, nanomedicine, and related fields. The scenario that relies on the interconnection of natural and artificial entities is briefly introduced, highlighting how Synthetic Biology (SB) plays a central role. SB allows the construction of various types of SCs that can be designed, tailored, and programmed according to specific predefined requirements. In particular, "bottom-up" SCs are briefly described by commenting on the principles of their design and fabrication and their features (in particular, the capacity to exchange chemicals with other SCs or with natural biological cells). Although bottom-up SCs still have low complexity and thus basic functionalities, here, we introduce their potential role in the IoBNT. This perspective paper aims to stimulate interest in and discussion on the presented topics. The article also includes commentaries on MC, semantic information, minimal cognition, wetware neuromorphic engineering, and chemical social robotics, with the specific potential they can bring to the IoBNT. [ABSTRACT FROM AUTHOR]

We present a rigorous and precise analysis of the maximum degree and the average degree in a dynamic duplication-divergence graph model introduced by Sol\'e et al. [Adv. Complex Syst., 5 (2002), pp. 43-54] in which the graph grows according to a duplication-divergence mechanism, i.e., by iteratively creating a copy of some node and then randomly alternating the neighborhood of a new node with probability p. This model captures the growth of some real-world processes, e.g., biological or social networks. In this paper, we prove that for some 0 < p < 1, the maximum degree and the average degree of a duplication-divergence graph on t vertices are asymptotically concentrated with high probability around tp and max\{ t2p-1, 1}, respectively, i.e., they are within at most a polylogarithmic factor from these values with probability at least 1-t-A for any constant A >0. [ABSTRACT FROM AUTHOR]

Centrality measurement plays an important role to identify important/influential vertices and edges in a network or graph from different points of view. It also provide invaluable insights into the structure and functioning of interconnected systems, enabling researchers to identify critical nodes for targeted interventions, predict network behaviors, and optimize network performance. Though there are different centrality measurements in graphs theory, yet closeness centrality is widely used to analyze biological networks, social networks, fuzzy social network, transportation networks, etc. The closeness centrality of a node x in a network/graph is the unit fraction whose denominator is the sum of the distances from x to other nodes. This paper presents theoretical development to compute the closeness centrality of each node/vertex of different corona product graphs between well known graph (path graph, complete graph, cycle graph, wheel graph, star graph and complete bipartite graph) and general graph. Corona graph has lots of applications in signed networks, biotechnology, chemistry, small-world network, etc. We also present a suitable real application of our proposed results by which we can identify the influential nodes in small-world network. [ABSTRACT FROM AUTHOR]

Background: There is an increasing interest in the use of Deep Learning (DL) based methods as a supporting analytical framework in oncology. However, most direct applications of DL will deliver models with limited transparency and explainability, which constrain their deployment in biomedical settings. Methods: This systematic review discusses DL models used to support inference in cancer biology with a particular emphasis on multi-omics analysis. It focuses on how existing models address the need for better dialogue with prior knowledge, biological plausibility and interpretability, fundamental properties in the biomedical domain. For this, we retrieved and analyzed 42 studies focusing on emerging architectural and methodological advances, the encoding of biological domain knowledge and the integration of explainability methods. Results: We discuss the recent evolutionary arch of DL models in the direction of integrating prior biological relational and network knowledge to support better generalisation (e.g. pathways or Protein-Protein-Interaction networks) and interpretability. This represents a fundamental functional shift towards models which can integrate mechanistic and statistical inference aspects. We introduce a concept of bio-centric interpretability and according to its taxonomy, we discuss representational methodologies for the integration of domain prior knowledge in such models. Conclusions: The paper provides a critical outlook into contemporary methods for explainability and interpretability used in DL for cancer. The analysis points in the direction of a convergence between encoding prior knowledge and improved interpretability. We introduce bio-centric interpretability which is an important step towards formalisation of biological interpretability of DL models and developing methods that are less problem- or application-specific. [ABSTRACT FROM AUTHOR]

Motivation Many ophthalmic disease biomarkers have been identified through comprehensive multiomics profiling, and hold significant potential in advancing the diagnosis, prognosis, and management of diseases. Meanwhile, the eye itself serves as a natural biomarker for several systemic diseases including neurological, renal, and cardiovascular systems. We aimed to collect and standardize this eye biomarkers information and construct the eye biomarker database (EBD) to provide ophthalmologists with a platform to search, analyze, and download these eye biomarker data. Results In this study, we present the EBD < http://www.eyeseeworld.com/ebd/index.html >, a world-first online compilation comprising 889 biomarkers for 26 ocular diseases and 939 eye biomarkers for 181 systemic diseases. The EBD also includes the information of 78 "nonbiomarkers"—the objects that have been proven cannot be biomarkers. Biological function and network analysis were conducted for these ocular disease biomarkers, and several hub pathways and common network topology characteristics were newly identified, which may promote future ocular disease biomarker discovery and characterizes the landscape of biomarkers for eye diseases at the pathway and network level. The EBD is expected to yield broader utility among developmental biologists and clinical scientists in and outside of the eye field by assisting in the identification of biomarkers linked to eye disorders and related systemic diseases. Availability and implementation EBD is available at http://www.eyeseeworld.com/ebd/index.html. [ABSTRACT FROM AUTHOR]

Graphs are used in various disciplines such as telecommunication, biological networks, as well as social networks. In large-scale networks, it is challenging to detect the communities by learning the distinct properties of the graph. As deep learning hasmade contributions in a variety of domains,we try to use deep learning techniques to mine the knowledge from large-scale graph networks. In this paper, we aim to provide a strategy for detecting communities using deep autoencoders and obtain generic neural attention to graphs. The advantages of neural attention are widely seen in the field of NLP and computer vision, which has low computational complexity for large-scale graphs. The contributions of the paper are summarized as follows. Firstly, a transformer is utilized to downsample the first-order proximities of the graph into a latent space, which can result in the structural properties and eventually assist in detecting the communities. Secondly, the fine-tuning task is conducted by tuning variant hyperparameters cautiously, which is applied to multiple social networks (Facebook and Twitch). Furthermore, the objective function (crossentropy) is tuned by L0 regularization. Lastly, the reconstructed model forms communities that present the relationship between the groups. The proposed robust model provides good generalization and is applicable to obtaining not only the community structures in social networks but also the node classification. The proposed graph-transformer shows advanced performance on the social networks with the average NMIs of 0.67±0.04, 0.198±0.02, 0.228±0.02, and 0.68±0.03 on Wikipedia crocodiles, Github Developers, Twitch England, and Facebook Page-Page networks, respectively. [ABSTRACT FROM AUTHOR]

Soil formation is the result of a complex network of biological as well as chemical and physical processes. Mainly the role of soil microbes is of high interest in this respect, as they are responsible for most transformations and drive the development of stable and labile carbon and nutrient pools in soil, which facilitate the basis for the subsequent establishment of plant communities. Glacier forefields, which provide a chronosequence of soils of different age due to the continuous retreat of the ice layer as a consequence of the increasing annual temperature since the last centuries, are a nice play ground to study the interaction of bacteria, fungi and archaea with their abiotic environment at different stages of soil formation. In this review we give insights into the role of microbes for soil development on the basis of investigations which have been performed at the Damma glacier in Switzerland in the frame of two international network projects Big Link (http://www.cces.ethz.ch/projects/clench/BigLink) and DFG SFB/TRR 38 (http://www.tu-cottbus.de/ecosystem). The review focusses on the microbiology of three major steps of soil formation including weathering of the parental material, the development of basic nutrient cycles, the formation of soil crusts and biofilms as initial microbial network structures and the occurrence of plants respectively the setup of plant communities. [ABSTRACT FROM AUTHOR]

A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following inheritance result is proved: under mild assumptions, splitting chemical reactions and inserting complexes involving some new chemical species preserves the capacity of a mass action CRN for multiple nondegenerate equilibria and/or periodic orbits. The claim has been proved previously for equilibria alone; however, the generalisation to include oscillation involves extensive development of rather different techniques. Several inheritance results for multistationarity and oscillation in mass action CRNs, including the main result of this paper, are gathered into a single theorem. Examples are presented showing how these results can be used together to make claims about reaction networks based on knowledge of their subnetworks. The examples include some networks of biological importance. [ABSTRACT FROM AUTHOR]

In this paper, the finite‐time observability (FO) of probabilistic Boolean control networks (PBCNs) based on set reachability and parallel extension is investigated. Under algebraic state space representation of PBCNs, finite‐time set reachability (FSR), finite‐time single input sequence set reachability (FSSSR), finite‐time arbitrary input sequence set reachability (FASSR), as well as finite‐time output feedback set reachability (FOSR) are addressed, where some efficient criteria are proposed. In the second part of this paper, several types of FO are provided, which can be converted to the corresponding FSR based on the parallel extension technique. Consequently, the obtained results for FSR are utilized to deal with FO. Finally, two examples including a biological network are given to demonstrate the theoretical results. [ABSTRACT FROM AUTHOR]

From this portal page, our readers can choose the journals they want to read, and manuscript authors can select the most suitable journals for their submissions by comparing the journal scopes, objectives, and recent papers. Furthermore, the editors of the three journals can recommend authors to transfer their manuscripts to another of the three journals if the submitted manuscript better matches their scopes and targets. Early View articles are complete full-text articles published online in advance of their publication in a printed issue. [Extracted from the article]

Spermbots are robotic sperms formed out of sperm cells conjugated to artificial microstructures, having potential applications ranging from biomedical processes, drug delivery systems, in situ real time imagery and assisted reproduction. The robotic sperm can act as an exploratory microdevice in biological networks. Incorporation of a biological entity like sperm into microstructures under the environment of magnetic or electric fields helps in shape templating and carrying chemotherapeutic agents to target sites. Besides its role in drug delivery systems, spermbots can potentially contribute in combating infertility, especially in oligo-zoospermia and necro-zoospermia in males. Numerous checkpoints may impede sperm cells to reach the oocyte in vivo. Spermbots bypass these sites and carry sperm to oocyte. Targeted delivery always requires interventions of natural functional aspects of living systems. Sperm flagellum, being a biological motor in nature, can be harnessed as a driving force in spermbots to ensure delivery of fertile sperm cells with impaired motile machinery to the target. Moreover, the technology has a potential to unravel sperm migration patterns and understanding the processes in vivo. After a review of documented literature on possible use of spermbot technology in assisted reproduction, we hereby discuss the application of this new and innovative technology in humans and animals. The paper also highlights certain shortfalls in the widespread application of this cargo delivery technology in assisted reproduction. [ABSTRACT FROM AUTHOR]

Proteins are important parts of the biological structures and encode a lot of biological information. Protein–protein interaction network alignment is a model for analyzing proteins that helps discover conserved functions between organisms and predict unknown functions. In particular, multi-network alignment aims at finding the mapping relationship among multiple network nodes, so as to transfer the knowledge across species. However, with the increasing complexity of PPI networks, how to perform network alignment more accurately and efficiently is a new challenge. This paper proposes a new global network alignment algorithm called Simulated Annealing Multiple Network Alignment (SAMNA), using both network topology and sequence homology information. To generate the alignment, SAMNA first generates cross-network candidate clusters by a clustering algorithm on a k-partite similarity graph constructed with sequence similarity information, and then selects candidate cluster nodes as alignment results and optimizes them using an improved simulated annealing algorithm. Finally, the SAMNA algorithm was experimented on synthetic and real-world network datasets, and the results showed that SAMNA outperformed the state-of-the-art algorithm in biological performance. [ABSTRACT FROM AUTHOR]

Link prediction in complex networks has recently attracted a great deal of attraction in diverse scientific domains, including social and biological sciences. Given a snapshot of a network, the goal is to predict links that are missing in the network or that are likely to occur in the near future. This problem has both theoretical and practical significance; it not only helps us to identify missing links in a network more efficiently by avoiding the expensive and time consuming experimental processes, but also allows us to study the evolution of a network with time. To address the problem of link prediction, numerous attempts have been made over the recent years that exploit the local and the global topological properties of the network to predict missing links in the network. In this paper, we use parametrised matrix forest index (PMFI) to predict missing links in a network. We show that, for small parameter values, this index is linked to a heat diffusion process on a graph and therefore encodes geometric properties of the network. We then develop a framework that combines the PMFI with a local similarity index to predict missing links in the network. The framework is applied to numerous networks obtained from diverse domains such as social network, biological network, and transport network. The results show that the proposed method can predict missing links with higher accuracy when compared to other state-of-the-art link prediction methods. [ABSTRACT FROM AUTHOR]

In modern biology, new knowledge is generated quickly, making it challenging for researchers to efficiently acquire and synthesise new information from the large volume of primary publications. To address this problem, computational approaches that generate machine-readable representations of scientific findings in the form of knowledge graphs have been developed. These representations can integrate different types of experimental data from multiple papers and biological knowledge bases in a unifying data model, providing a complementary method to manual review for interacting with published knowledge. The Gene Ontology Consortium (GOC) has created a semantic modelling framework that extends individual functional gene annotations to structured descriptions of causal networks representing biological processes (Gene Ontology–Causal Activity Modelling, or GO–CAM). In this study, we explored whether the GO–CAM framework could represent knowledge of the causal relationships between environmental inputs, neural circuits and behavior in the model nematode C. elegans [C. elegans Neural–Circuit Causal Activity Modelling (CeN–CAM)]. We found that, given extensions to several relevant ontologies, a wide variety of author statements from the literature about the neural circuit basis of egg-laying and carbon dioxide (CO2) avoidance behaviors could be faithfully represented with CeN–CAM. Through this process, we were able to generate generic data models for several categories of experimental results. We also discuss how semantic modelling may be used to functionally annotate the C. elegans connectome. Thus, Gene Ontology-based semantic modelling has the potential to support various machine-readable representations of neurobiological knowledge. [ABSTRACT FROM AUTHOR]

The study of comorbidity can provide new insights into the pathogenesis of the disease and has important economic significance in the clinical evaluation of treatment difficulty, medical expenses, length of stay, and prognosis of the disease. In this paper, we propose a disease association prediction model DapBCH, which constructs a cross-species biological network and applies heterogeneous graph embedding to predict disease association. First, we combine the human disease-gene network, mouse gene-phenotype network, human-mouse homologous gene network, and human protein-protein interaction network to reconstruct a heterogeneous biological network. Second, we apply heterogeneous graph embedding based on meta-path aggregation to generate the feature vector of disease nodes. Finally, we employ link prediction to obtain the similarity of disease pairs. The experimental results indicate that our model is highly competitive in predicting the disease association and is promising for finding potential disease associations. [ABSTRACT FROM AUTHOR]

Over the last couple of decades, Social Networks have connected people on the web from across the globe and have become a crucial part of our daily life. These networks have also rapidly grown as platforms for propagating products, ideas, and opinions to target a wider audience. This calls for the need to find influential nodes in a network for a variety of reasons, including the curb of misinformation being spread across the networks, advertising products efficiently, finding prominent protein structures in biological networks, etc. In this paper, we propose Modified Community Diversity (MCD), a novel method for finding influential nodes in a network by exploiting community detection and a modified community diversity approach. We extend the concept of community diversity to a two-hop scenario. This helps us evaluate a node's possible influence over a network more accurately and also avoids the selection of seed nodes with an overlapping scope of influence. Experimental results verify that MCD outperforms various other state-of-the-art approaches on eight datasets cumulatively across three performance metrics. [ABSTRACT FROM AUTHOR]

How to represent and discover social links from the perspective of implied behaviors, in particular latent links, is critical for social media analysis. In this paper, we discuss latent link analysis for community detection in social behavioral interactions. We adopt Markov network (MN) as the framework and propose the algorithm to discover latent links among social objects implied in their behavioral interactions without regard for the topological structures of social networks. First, starting from the frequent itemsets of the behavioral interactions, we propose the algorithm to construct the item-association Markov network (IAMN), which establishes the inherent relationship between frequent itemset and MN. Then, we propose the algorithm to detect communities by incorporating the concepts of k-clique and k-nearest neighbor set, as the typical application of the constructed IAMN Experimental results show the effectiveness and efficiency of the method proposed in this paper. [ABSTRACT FROM AUTHOR]

Summary: In this paper, a link is proposed for wireless body area sensor networks (WBASNs) for the transmission of electrocardiogram (ECG) signal. When the quantity of signal is very high, then it is beneficial that signal should be compressed before transmission. In that situation, the signal compression and error control schemes played an important role in the designing of link for WBASNs. In case of biological sensor network, it is very important that node consumed less power in transmission because the replacement of nodes is a very complex surgical procedure in many medical situations. A compressed sensing concept is introduced here. The main aspect of this paper is to present transmission strategy that provides fast and accurate transmission of ECG signals. In this the smart sensor nodes are utilized. These nodes having sensing, transformation and transmission capability. The nodes sense the ECG signals, and these signal are compressed by Walsh–Hadamard transform method. This compressed signal is transmitted to the module outside the human body. In this module, various error control coding and modulation operations are to be performed on signals, and after that, signals are transmitted to the final destination. The compressed signal occupied less storage space, and ECC provides high data rate. In that manner, the fast transmission of ECG data becomes possible on low data rate sensor network link. [ABSTRACT FROM AUTHOR]

A major goal in genomics is to properly capture the complex dynamical behaviors of gene regulatory networks (GRNs). This includes inferring the complex interactions between genes, which can be used for a wide range of genomics analyses, including diagnosis or prognosis of diseases and finding effective treatments for chronic diseases such as cancer. Boolean networks have emerged as a successful class of models for capturing the behavior of GRNs. In most practical settings, inference of GRNs should be achieved through limited and temporally sparse genomics data. A large number of genes in GRNs leads to a large possible topology candidate space, which often cannot be exhaustively searched due to the limitation in computational resources. This paper develops a scalable and efficient topology inference for GRNs using Bayesian optimization and kernel-based methods. Rather than an exhaustive search over possible topologies, the proposed method constructs a Gaussian Process (GP) with a topology-inspired kernel function to account for correlation in the likelihood function. Then, using the posterior distribution of the GP model, the Bayesian optimization efficiently searches for the topology with the highest likelihood value by optimally balancing between exploration and exploitation. The performance of the proposed method is demonstrated through comprehensive numerical experiments using a well-known mammalian cell-cycle network. [ABSTRACT FROM AUTHOR]

Simple Summary: The growing evidence suggested that competing endogenous RNAs (ceRNAs) have significant associations with tumor occurrence and progression, yet the regulatory mechanism of them in lung adenocarcinoma remains unclear. Identification of the regulatory modules for lung adenocarcinoma is a critical and fundamental step towards understanding the regulatory mechanisms during carcinogenesis. Deep neural network (DNN) models have become a powerful tool to intelligently recognize the sophisticated relationships of ceRNAs appropriately. In this paper, multiple deep neural network models were constructed using the expression data to identify regulatory modules for lung adenocarcinoma in biological networks. Three identified regulatory modules association with lung adenocarcinoma were validated from three aspects, i.e., literature review, functional enrichment analysis, and an independent dataset. The regulatory relationships between RNAs were validated in various datasets, including CPTAC, TCGA and an expression profile from the GEO database. Our study will contribute to improving the understanding of regulatory mechanisms in the carcinogenesis of lung adenocarcinoma and provide schemes for identifying novel regulatory modules of other cancers. Lung adenocarcinoma is the most common type of primary lung cancer, but the regulatory mechanisms during carcinogenesis remain unclear. The identification of regulatory modules for lung adenocarcinoma has become one of the hotspots of bioinformatics. In this paper, multiple deep neural network (DNN) models were constructed using the expression data to identify regulatory modules for lung adenocarcinoma in biological networks. First, the mRNAs, lncRNAs and miRNAs with significant differences in the expression levels between tumor and non-tumor tissues were obtained. MRNA DNN models were established and optimized to mine candidate mRNAs that significantly contributed to the DNN models and were in the center of an interaction network. Another DNN model was then constructed and potential ceRNAs were screened out based on the contribution of each RNA to the model. Finally, three modules comprised of miRNAs and their regulated mRNAs and lncRNAs with the same regulation direction were identified as regulatory modules that regulated the initiation of lung adenocarcinoma through ceRNAs relationships. They were validated by literature and functional enrichment analysis. The effectiveness of these regulatory modules was evaluated in an independent lung adenocarcinoma dataset. Regulatory modules for lung adenocarcinoma identified in this study provided a reference for regulatory mechanisms during carcinogenesis. [ABSTRACT FROM AUTHOR]

In recent years, neural networks have attracted much attention in the machine learning and the deep learning technologies. Bio-inspired functions and intelligence are also expected to process efficiently and improve existing technologies. In the visual pathway, the prominent features consist of nonlinear characteristics of squaring and rectification functions observed in the retinal and visual cortex networks, respectively. Further, adaptation is an important feature to activate the biological systems, efficiently. Recently, to overcome short-comings of the deep learning techniques, orthogonality for the weights in the networks has been developed for the signal propagation and the efficient optimization of the learning. In this paper, bio-inspired asymmetric networks with nonlinear characteristics are proposed, which are derived from the retinal networks in the biological visual pathway. The asymmetric network proposed here was verified to detect the movement of the object, efficiently in our previous studies. This paper shows a new characteristic of the adaptive orthogonality in the asymmetric networks. First, it is shown that the asymmetric network with nonlinear characteristics is effective for generating orthogonality. Second, the proposed asymmetric network with Gabor filters is compared with the conventional energy model from the point of the orthogonality characteristics. Finally, the asymmetric networks with nonlinear characteristics can generate the extended orthogonal bases in independent subspaces, which are useful for classification and efficient learning. [ABSTRACT FROM AUTHOR]

The 17th International NETTAB workshop was held in Palermo, Italy, on October 16-18, 2017. The special topic for the meeting was "Methods, tools and platforms for Personalised Medicine in the Big Data Era", but the traditional topics of the meeting series were also included in the event. About 40 scientific contributions were presented, including four keynote lectures, five guest lectures, and many oral communications and posters. Also, three tutorials were organised before and after the workshop. Full papers from some of the best works presented in Palermo were submitted for this Supplement of BMC Bioinformatics. Here, we provide an overview of meeting aims and scope. We also shortly introduce selected papers that have been accepted for publication in this Supplement, for a complete presentation of the outcomes of the meeting. [ABSTRACT FROM AUTHOR]

During travelling, more and more information must be taken into account, and travelers have to make several complex decisions. In order to support these decisions, IT solutions are unavoidable, and as the computational demand is constantly growing, the examination of state-of-the-art methodologies is necessary. In our research, a parallelized Ant Colony algorithm was investigated, and a parameter study on a real network has been made. The aim was to inspect the sensibility of the method and to demonstrate its applicability in a multi-threaded system (e.g. Cloud-based systems). Based on the research, increased effectiveness can be reached by using more threads. The novelty of the paper is the usage of the processors' parallel computing capability for routing with the Ant Colony algorithm. [ABSTRACT FROM AUTHOR]

Background: Gene co-expression networks (GCNs) are not easily comparable due to their complex structure. In this paper, we propose a tool, Juxtapose, together with similarity measures that can be utilized for comparative transcriptomics between a set of organisms. While we focus on its application to comparing co-expression networks across species in evolutionary studies, Juxtapose is also generalizable to co-expression network comparisons across tissues or conditions within the same species. Methods: A word embedding strategy commonly used in natural language processing was utilized in order to generate gene embeddings based on walks made throughout the GCNs. Juxtapose was evaluated based on its ability to embed the nodes of synthetic structures in the networks consistently while also generating biologically informative results. Evaluation of the techniques proposed in this research utilized RNA-seq datasets from GTEx, a multi-species experiment of prefrontal cortex samples from the Gene Expression Omnibus, as well as synthesized datasets. Biological evaluation was performed using gene set enrichment analysis and known gene relationships in literature. Results: We show that Juxtapose is capable of globally aligning synthesized networks as well as identifying areas that are conserved in real gene co-expression networks without reliance on external biological information. Furthermore, output from a matching algorithm that uses cosine distance between GCN embeddings is shown to be an informative measure of similarity that reflects the amount of topological similarity between networks. Conclusions: Juxtapose can be used to align GCNs without relying on known biological similarities and enables post-hoc analyses using biological parameters, such as orthology of genes, or conserved or variable pathways. Availability: A development version of the software used in this paper is available at https://github.com/klovens/juxtapose [ABSTRACT FROM AUTHOR]

Motivation: Recent advances in spatially resolved transcriptomics (ST) technologies enable the measurement of gene expression profiles while preserving cellular spatial context. Linking gene expression of cells with their spatial distribution is essential for better understanding of tissue microenvironment and biological progress. However, effectively combining gene expression data with spatial information to identify spatial domains remains challenging. Results: To deal with the above issue, in this paper, we propose a novel unsupervised learning framework named STMGCN for identifying spatial domains using multi-view graph convolution networks (MGCNs). Specifically, to fully exploit spatial information, we first construct multiple neighbor graphs (views) with different similarity measures based on the spatial coordinates. Then, STMGCN learns multiple view-specific embeddings by combining gene expressions with each neighbor graph through graph convolution networks. Finally, to capture the importance of different graphs, we further introduce an attention mechanism to adaptively fuse view-specific embeddings and thus derive the final spot embedding. STMGCN allows for the effective utilization of spatial context to enhance the expressive power of the latent embeddings with multiple graph convolutions. We apply STMGCN on two simulation datasets and five real spatial transcriptomics datasets with different resolutions across distinct platforms. The experimental results demonstrate that STMGCN obtains competitive results in spatial domain identification compared with five state-of-the-art methods, including spatial and non-spatial alternatives. Besides, STMGCN can detect spatially variable genes with enriched expression patterns in the identified domains. Overall, STMGCN is a powerful and efficient computational framework for identifying spatial domains in spatial transcriptomics data. [ABSTRACT FROM AUTHOR]

Many important aspects of biological knowledge at the molecular level can be represented by pathways. Through their analysis, we gain mechanistic insights and interpret lists of interesting genes from experiments (usually omics and functional genomic experiments). As a result, pathways play a central role in the development of bioinformatics methods and tools for computing predictions from known molecular-level mechanisms. Qualitative as well as quantitative knowledge about pathways can be effectively represented through biochemical networks linking the biochemical reactions and the compounds (e.g., proteins) occurring in the considered pathways. So, repositories providing biochemical networks for known pathways play a central role in bioinformatics and in systems biology. Here we focus on Reactome, a free, comprehensive, and widely used repository for biochemical networks and pathways. In this paper, we: (1) introduce a tool StARGate-X (STatistical Analysis of the Reactomemulti-GrAph ThroughnEtworkX) to carry out an automated analysis of the connectivity properties of Reactome biochemical reaction network and of its biological hierarchy (i.e., cell compartments, namely, the closed parts within the cytosol, usually surrounded by a membrane); the code is freely available at https://github.com/marinoandrea/stargate-x; (2) show the effectiveness of our tool by providing an analysis of the Reactome network, in terms of centrality measures, with respect to in- and out-degree. As an example of usage of StARGate-X, we provide a detailed automated analysis of the Reactome network, in terms of centrality measures. We focus both on the subgraphs induced by single compartments and on the graph whose nodes are the strongly connected components. To the best of our knowledge, this is the first freely available tool that enables automatic analysis of the large biochemical network within Reactome through easy-to-use APIs (Application Programming Interfaces). [ABSTRACT FROM AUTHOR]

Previous studies have inferred robust stability of reaction networks by utilizing linear programs or iterative algorithms. Such algorithms become tedious or computationally infeasible for large networks. In addition, they operate like black boxes without offering intuition for the structures that are necessary to maintain stability. In this work, we provide several graphical criteria for constructing robust stability certificates, checking robust non-degeneracy, verifying persistence, and establishing global stability. By characterizing a set of stability-preserving graph modifications that includes the enzymatic modification motif, we show that the stability of arbitrarily large nonlinear networks can be examined by simple visual inspection. We show applications of this technique to ubiquitous motifs in systems biology such as post-translational modification (PTM) cycles, the ribosome flow model (RFM), T-cell kinetic proofreading, and others. The results of this paper are dedicated in honor of Eduardo D. Sontag's seventieth birthday and his pioneering work in nonlinear dynamical systems and mathematical systems biology. [ABSTRACT FROM AUTHOR]

Essential proteins are vital for maintaining life activities and play a crucial role in biological processes. Identifying essential proteins is of utmost importance as it helps in understanding the minimal requirements for cell life, discovering pathogenic genes and drug targets, diagnosing diseases, and comprehending the mechanism of biological evolution. The latest research suggests that integrating protein–protein interaction (PPI) networks and relevant biological sequence features can enhance the accuracy and robustness of essential protein identification. In this paper, a deep neural network (DNN) method was used to identify a yeast essential protein, which was named IYEPDNN. The method combines gene expression profiles, PPI networks, and orthology as input features to improve the accuracy of DNN while reducing computational complexity. To enhance the robustness of the yeast dataset, the common least squares method is used to supplement absenting data. The correctness and effectiveness of the IYEPDNN method are verified using the DIP and GAVIN databases. Our experimental results demonstrate that IYEPDNN achieves an accuracy of 84%, and it outperforms state-of-the-art methods (WDC, PeC, OGN, ETBUPPI, RWAMVL, etc.) in terms of the number of essential proteins identified. The findings of this study demonstrate that the correlation between features plays a crucial role in enhancing the accuracy of essential protein prediction. Additionally, selecting the appropriate training data can effectively address the issue of imbalanced training data in essential protein identification. [ABSTRACT FROM AUTHOR]

A wealth of causal relationships exists in biological systems, both causal brain networks and causal protein signaling networks are very classical causal biological networks (CBNs). Learning CBNs from biological signal data reliably is a critical problem today. However, most of the existing methods are not excellent enough in terms of accuracy and time performance, and tend to fall into local optima because they do not take full advantage of global information. In this paper, we propose a parallel ant colony optimization algorithm to learn causal biological networks from biological signal data, called PACO. Specifically, PACO first maps the construction of CBNs to ants, then searches for CBNs in parallel by simulating multiple groups of ants foraging, and finally obtains the optimal CBN through pheromone fusion and CBNs fusion between different ant colonies. Extensive experimental results on simulation data sets as well as two real-world data sets, the fMRI signal data set and the Single-cell data set, show that PACO can accurately and efficiently learn CBNs from biological signal data. [ABSTRACT FROM AUTHOR]

The popularity of social networks is growing and offering promising opportunities for practical applications, such as computer networks, social systems, physical systems, and biological networks. The use of networks provides valuable insights into the patterns, relationships, and behavior of various entities and their interactions. Healthcare service systems are critical social systems that can be analyzed using network-based methodologies, one of which is influence maximization (IM). It is a network analysis technique that identifies a small subset of suppliers in a network that has the most influence on the overall behavior of the healthcare system. By utilizing network analysis techniques, data scientists can identify the most crucial healthcare providers in a network and better understand the system's operation. The paper uses a network global structure-based centrality (ngsc) approach that combines conventional k-shell and the sum of neighbors' degree methods with information about the network's global structural features to identify significant providers in the provider-interacting network. The experimental outcomes on five real-world networks reveal that the proposed NGSC technique outperforms earlier benchmark methods in identifying significant providers under a spreading dynamic when using the IC model. [ABSTRACT FROM AUTHOR]

Mathematical modeling of the emergent dynamics of gene regulatory networks (GRN) faces a double challenge of (a) dependence of model dynamics on parameters, and (b) lack of reliable experimentally determined parameters. In this paper we compare two complementary approaches for describing GRN dynamics across unknown parameters: (1) parameter sampling and resulting ensemble statistics used by RACIPE (RAndom CIrcuit PErturbation), and (2) use of rigorous analysis of combinatorial approximation of the ODE models by DSGRN (Dynamic Signatures Generated by Regulatory Networks). We find a very good agreement between RACIPE simulation and DSGRN predictions for four different 2- and 3-node networks typically observed in cellular decision making. This observation is remarkable since the DSGRN approach assumes that the Hill coefficients of the models are very high while RACIPE assumes the values in the range 1-6. Thus DSGRN parameter domains, explicitly defined by inequalities between systems parameters, are highly predictive of ODE model dynamics within a biologically reasonable range of parameters. [ABSTRACT FROM AUTHOR]

The variation of the network topology directly indicates the knowledge network evolution, the principal composition of which is the structural evolution. Based on the principles of both the minimum coupling costs between knowledge subjects and the network average value threshold, this paper constructs the evolution model of a small-world knowledge network. Using MATLAB programming, this paper analyzes the characteristics of the evolution of knowledge network. It then examines the main parameter changes and the distribution of the network node degree as well as its probability distribution and then proceeds to investigate the variation of the subjects' knowledge level as well as the variation speed. The simulation results show that with the structural evolution of the knowledge network, the connection between the network subjects has been improved after numerous rewiring. Compared with the initial state, the total knowledge stock of the knowledge network and the average knowledge stock of the subjects are significantly enhanced. [ABSTRACT FROM AUTHOR]

Multiple sclerosis (MS) is an autoimmune disease for which it is difficult to find exact disease-related genes. Effectively identifying disease-related genes would contribute to improving the treatment and diagnosis of multiple sclerosis. Current methods for identifying disease-related genes mainly focus on the hypothesis of guilt-by-association and pay little attention to the global topological information of the whole protein-protein-interaction (PPI) network. Besides, network representation learning (NRL) has attracted a huge amount of attention in the area of network analysis because of its promising performance in node representation and many downstream tasks. In this paper, we try to introduce NRL into the task of disease-related gene prediction and propose a novel framework for identifying the disease-related genes multiple sclerosis. The proposed framework contains three main steps: capturing the topological structure of the PPI network using NRL-based methods, encoding learned features into low-dimensional space using a stacked autoencoder, and training a support vector machine (SVM) classifier to predict disease-related genes. Compared with three state-of-the-art algorithms, our proposed framework shows superior performance on the task of predicting disease-related genes of multiple sclerosis. [ABSTRACT FROM AUTHOR]