Cluster Topology Research Articles

Integration of Heuristics-Based Energy Optimal Clustering Topology, Routing and Transmission Scheduling for Enhancing Lifetime in IoT Networks

Integration of Heuristics-Based Energy Optimal Clustering Topology, Routing and Transmission Scheduling for Enhancing Lifetime in IoT Networks

Programmable photonic integrated meshes for modular generation of optical entanglement links

Large-scale generation of quantum entanglement between individually controllable qubits is at the core of quantum computing, communications, and sensing. Modular architectures of remotely-connected quantum technologies have been proposed for a variety of physical qubits, with demonstrations reported in atomic and all-photonic systems. However, an open challenge in these architectures lies in constructing high-speed and high-fidelity reconfigurable photonic networks for optically-heralded entanglement among target qubits. Here we introduce a programmable photonic integrated circuit (PIC), realized in a piezo-actuated silicon nitride (SiN)-in-oxide CMOS-compatible process, that implements an N × N Mach–Zehnder mesh (MZM) capable of high-speed execution of linear optical transformations. The visible-spectrum photonic integrated mesh is programmed to generate optical connectivity on up to N = 8 inputs for a range of optically-heralded entanglement protocols. In particular, we experimentally demonstrated optical connections between 16 independent pairwise mode couplings through the MZM, with optical transformation fidelities averaging 0.991 ± 0.0063. The PIC’s reconfigurable optical connectivity suffices for the production of 8-qubit resource states as building blocks of larger topological cluster states for quantum computing. Our programmable PIC platform enables the fast and scalable optical switching technology necessary for network-based quantum information processors.

Opening the black-box of Neighbor Embeddings with Hotelling’s [formula omitted] statistic and [formula omitted]-residuals

In contrast to classical techniques for exploratory analysis of high-dimensional data sets, such as principal component analysis (PCA), neighbor embedding (NE) techniques tend to better preserve the local structure/topology of high-dimensional data. However, the ability to preserve local structure comes at the expense of interpretability: techniques such as t-Distributed Stochastic Neighbor Embedding (t-SNE) or Uniform Manifold Approximation and Projection (UMAP) do not provide insights into which input or to what extent the variables underlie the topological (cluster) structure seen in the corresponding embedding. We here introduce X-MAP, a workflow that employs different “tricks” from the chemometrics field based on PCA, Q-residuals and Hotelling’s T2 contributions in combination with novel visualization approaches to derive local and global explanations of neighbor embeddings. We show how our approach is capable of identifying discriminatory features between groups of data points that remain unnoticed when exploring NEs using standard univariate or multivariate approaches.

Excess BMI in early adolescence adversely impacts maturating functional circuits supporting high-level cognition and their structural correlates.

Adverse effects of excess BMI (affecting 1 in 5 children in the US) on brain circuits during neurodevelopmentally vulnerable periods are incompletely understood. This study investigated BMI-related alterations in maturating functional networks and their underlying brain structures, and high-level cognition in early adolescence. Cross-sectional resting-state fMRI, structural sMRI, neurocognitive task scores, and BMI from 4922 youth [median (IQR) age = 120.0 (13.0) months, 2572 females (52.25%)] from the Adolescent Brain Cognitive Development (ABCD) cohort were analyzed. Comprehensive topological and morphometric network properties were estimated from fMRI and sMRI, respectively. Cross-validated linear regression models assessed correlations with BMI. Results were reproduced across multiple fMRI datasets. Almost 30% of youth had excess BMI, including 736 (15.0%) with overweight and 672 (13.7%) with obesity, and statistically more Black and Hispanic compared to white, Asian and non-Hispanic youth (p < 0.01). Those with obesity or overweight were less physically active, slept less than recommended, snored more frequently, and spent more time using an electronic device (p < 0.01). They also had lower topological efficiency, resilience, connectivity, connectedness and clustering in Default-Mode, dorsal attention, salience, control, limbic, and reward networks (p ≤ 0.04, Cohen's d: 0.07-0.39). Lower cortico-thalamic efficiency and connectivity were estimated only in youth with obesity (p < 0.01, Cohen's d: 0.09-0.19). Both groups had lower cortical thickness, volume and white matter intensity in these networks' constituent structures, particularly anterior cingulate, entorhinal, prefrontal, and lateral occipital cortices (p < 0.01, Cohen's d: 0.12-0.30), which also mediated inverse relationships between BMI and regional functional topologies. Youth with obesity or overweight had lower scores in a task measuring fluid reasoning - a core aspect of cognitive function, which were partially correlated with topological changes (p ≤ 0.04). Excess BMI in early adolescence may be associated with profound aberrant topological alterations in maturating functional circuits and underdeveloped brain structures that adversely impact core aspects of cognitive function.

High-throughput Pore-C reveals the single-allele topology and cell type-specificity of 3D genome folding

Canonical three-dimensional (3D) genome structures represent the ensemble average of pairwise chromatin interactions but not the single-allele topologies in populations of cells. Recently developed Pore-C can capture multiway chromatin contacts that reflect regional topologies of single chromosomes. By carrying out high-throughput Pore-C, we reveal extensive but regionally restricted clusters of single-allele topologies that aggregate into canonical 3D genome structures in two human cell types. We show that fragments in multi-contact reads generally coexist in the same TAD. In contrast, a concurrent significant proportion of multi-contact reads span multiple compartments of the same chromatin type over megabase distances. Synergistic chromatin looping between multiple sites in multi-contact reads is rare compared to pairwise interactions. Interestingly, the single-allele topology clusters are cell type-specific even inside highly conserved TADs in different types of cells. In summary, HiPore-C enables global characterization of single-allele topologies at an unprecedented depth to reveal elusive genome folding principles.

An Energy-Efficient T-Based Routing Topology for Target Tracking in Battery Operated Mobile Wireless Sensor Networks.

Real-time smart applications are now possible because to developments in communication and sensor technology. Wireless sensor networks (WSNs) are used to collect data from specific disaster sites, such as fire events, gas leaks, land mines, earthquake, landslides, etc., where it is necessary to know the exact location of the detected information to safely rescue the people. For instance, the detection and disposal of explosive materials is a difficult task because land mines consistently threaten human life. Here, the T-based Routing Topology (TRT) is suggested to gather data from sensors (metal detectors, Ground Penetrating Radars (GPR), Infra-Red sensors, etc.), Global Positioning System (GPS), and cameras in land mine-affected areas. Buried explosive materials can be found and located with high accuracy. Additionally, it will be simpler to eliminate bombs and reduce threats to humans. The efficiency of the suggested data collection method is evaluated using Network Simulator-2 (NS-2). Also, the proposed T-based routing topology requires a minimal number of nodes to cover the entire searching area and establish effective communication. In contrast, the number of nodes participating in the sensing area grows, as the depth of the tree increases in the existing tree topology-based data gathering. And for cluster topology, the number of nodes deployment depends on the transmission range of the sensor nodes.

ICRA: An Intelligent Clustering Routing Approach for UAV Ad Hoc Networks

As an important means of obtaining information of marine situation, the marine monitoring system relying on UAV has been paid more and more attention by all countries in the world, and the demand for tasks is growing continually. In UAV ad hoc networks, routing protocols with immutable routing policies that lack flexibility are generally incapable of maintaining effective performance due to the complicated and rapidly changing environmental situation and application requirements. In this paper, we propose an intelligent clustering routing approach (ICRA) for UANETs. The ICRA is composed of three components: the clustering module, the clustering strategy adjustment module and the routing module. In the clustering process, each node needs to calculate its utility. In order to maintain high topology stability and long network lifetime in different network states, the reinforcement learning based clustering strategy adjustment module needs continuous learning the benefits brought by adopting different strategies to calculate the nodes utility in a specific network state. With the learned knowledge, clustering strategy adjustment module could determine the optimal clustering strategy according to the current network state. In the routing phase, the proposed scheme can reduce the end-to-end delay and improve the packet delivery rate by introducing inter-cluster forwarding nodes to forward messages among different clusters. Extensive experiments have been conducted to verify ICRA’s robustness and superiority over existing schemes. The results demonstrate that ICRA could achieve better performance than its state-of-the-art counterparts with regard to the clustering efficiency, topology stability, energy efficiency and quality of service.

Deep learning techniques for energy clustering in the CMS ECAL

The reconstruction of electrons and photons in CMS depends on topological clustering of the energy deposited by an incident particle in different crystals of the electromagnetic calorimeter (ECAL). These clusters are formed by aggregating neighbouring crystals according to the expected topology of an electromagnetic shower in the ECAL. The presence of upstream material (beampipe, tracker and support structures) causes electrons and photons to start showering before reaching the calorimeter. This effect, combined with the 3.8T CMS magnetic field, leads to energy being spread in several clusters around the primary one. It is essential to recover the energy contained in these satellite clusters in order to achieve the best possible energy resolution for physics analyses. Historically satellite clusters have been associated to the primary cluster using a purely topological algorithm which does not attempt to remove spurious energy deposits from additional pileup interactions (PU). The performance of this algorithm is expected to degrade during LHC Run 3 (2022+) because of the larger average PU levels and the increasing levels of noise due to the ageing of the ECAL detector. New methods are being investigated that exploit state-of-the-art deep learning architectures like Graph Neural Networks (GNN) and self-attention algorithms. These more sophisticated models improve the energy collection and are more resilient to PU and noise, helping to preserve the electron and photon energy resolution achieved during LHC Runs 1 and 2. This work will cover the challenges of training the models as well the opportunity that this new approach offers to unify the ECAL energy measurement with the particle identification steps used in the global CMS photon and electron reconstruction.

GPU acceleration of the ATLAS calorimeter clustering algorithm

Given the upcoming High-Luminosity LHC Upgrade, the performance requirements for the trigger systems associated with the LHC experiments will increase due to the larger volume of data to be processed. One of the possibilities that the ATLAS Collaboration is evaluating for upgrading the software-based portion of its trigger system is the use of Graphical Processing Units as hardware accelerators. The present work focuses on the GPU acceleration of the Topological Clustering algorithm, which is used to reconstruct calorimeter showers by grouping cells according to their signal-to-noise ratio. A more GPU parallelizable version of the Topological Clustering, called Topo-Automaton Clustering, was implemented within AthenaMT, the software framework of the ATLAS trigger, and its results were compared to those of the standard CPU algorithm to ensure physical validity is maintained. Time measurements suggest an average improvement of the event processing time by a factor between 3.5 and 5.5 (depending on the kind of the event), though less than 20% of that time corresponds to the algorithm itself, suggesting that the main bottleneck lies in data transfers and conversions.

Network pharmacology study of the mechanism underlying the therapeutic effect of Zhujing pill and its main component oleanolic acid against diabetic retinopathy.

Diabetic retinopathy (DR) is the leading cause of blindness in the working population worldwide, with few effective drugs available for its treatment in the early stages. The Zhujing pill (ZJP) is well-established to enhance the early symptoms of DR, but the mechanism underlying its therapeutic effect remains unclear. In the present study, we used systems biology and multidirectional pharmacology to screen the main active ingredients of ZJP and retrieved DrugBank and Genecards databases to obtain 'drug-disease' common targets. Using bioinformatics analysis, we obtained the core targets, and potential mechanisms of action of ZJP and its main components for the treatment of DR. Molecular docking was used to predict the binding sites and the binding affinity of the main active ingredients to the core targets. The predicted mechanism was verified in animal experiments. We found that the main active ingredient of ZJP was oleanolic acid, and 63 common 'drug-disease' targets were identified. Topological analysis and cluster analysis based on the protein-protein interaction network of the Metascape database screened the core targets as PRKCA, etc. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these core targets were significantly enriched in the pro-angiogenic pathway of the VEGF signaling pathway. Molecular docking and surface plasmon resonance revealed that ZJP and its main active component, oleanolic acid had the highest binding affinity with PKC-α, the core target of the VEGF signaling pathway. Animal experiments validated that ZJP and oleanolic acid could improve DR.

Short-Term Head-Out Whole-Body Cold-Water Immersion Facilitates Positive Affect and Increases Interaction between Large-Scale Brain Networks.

An emerging body of evidence indicates that short-term immersion in cold water facilitates positive affect and reduces negative affect. However, the neural mechanisms underlying these effects remain largely unknown. For the first time, we employed functional magnetic resonance imaging (fMRI) to identify topological clusters of networks coupled with behavioural changes in positive and negative affect after a 5 min cold-water immersion. Perceived changes in positive affect were associated with feeling more active, alert, attentive, proud, and inspired, whilst changes in negative affect reflected reductions in distress and nervousness. The increase in positive affect was supported by a unique component of interacting networks, including the medial prefrontal node of the default mode network, a posterior parietal node of the frontoparietal network, and anterior cingulate and rostral prefrontal parts of the salience network and visual lateral network. This component emerged as a result of a focal effect confined to few connections. Changes in negative affect were associated with a distributed component of interacting networks at a reduced threshold. Affective changes after cold-water immersion occurred independently, supporting the bivalence model of affective processing. Interactions between large-scale networks linked to positive affect indicated the integrative effects of cold-water immersion on brain functioning.

Network-based validation of the psychometric questionnaire EDI-3 for the assessment of eating disorders

Assessing the validity of a psychometric test is fundamental to ensure a reliable interpretation of its outcomes. Few attempts have been made recently to complement classical approaches (e.g., factor models) with a novel technique based on network analysis. The objective of the current study is to carry out a network-based validation of the Eating Disorder Inventory 3 (EDI-3), a questionnaire designed for the assessment of eating disorders. Exploiting a reliable, open source sample of 1206 patients diagnosed with an eating disorder, we set up a robust validation process encompassing detection and handling of redundant EDI-3 items, estimation of the cross-sample psychometric network, resampling bootstrap procedure and computation of the median network of the replica samples. We then employed a community detection algorithm to identify the topological clusters, evaluated their coherence with the EDI-3 subscales and replicated the full validation analysis on the subpopulations corresponding to patients diagnosed with either anorexia nervosa or bulimia nervosa. Results of the network-based analysis, and particularly the topological community structures, provided support for almost all the composite scores of the EDI-3 and for 2 single subscales: Bulimia and Maturity Fear. A moderate instability of some dimensions led to the identification of a few multidimensional items that should be better located in the intersection of multiple psychological scales. We also found that, besides symptoms typically attributed to eating disorders, such as drive for thinness, also non-specific symptoms like low self-esteem and interoceptive deficits play a central role in both the cross-sample and the diagnosis-specific networks. Our work adds insights into the complex and multidimensional structure of EDI-3 by providing support to its network-based validity on both mixed and diagnosis-specific samples. Moreover, we replicated previous results that reinforce the transdiagnostic theory of eating disorders.

Topological identification and interpretation for single-cell gene regulation elucidation across multiple platforms using scMGCA

Single-cell RNA sequencing provides high-throughput gene expression information to explore cellular heterogeneity at the individual cell level. A major challenge in characterizing high-throughput gene expression data arises from challenges related to dimensionality, and the prevalence of dropout events. To address these concerns, we develop a deep graph learning method, scMGCA, for single-cell data analysis. scMGCA is based on a graph-embedding autoencoder that simultaneously learns cell-cell topology representation and cluster assignments. We show that scMGCA is accurate and effective for cell segregation and batch effect correction, outperforming other state-of-the-art models across multiple platforms. In addition, we perform genomic interpretation on the key compressed transcriptomic space of the graph-embedding autoencoder to demonstrate the underlying gene regulation mechanism. We demonstrate that in a pancreatic ductal adenocarcinoma dataset, scMGCA successfully provides annotations on the specific cell types and reveals differential gene expression levels across multiple tumor-associated and cell signalling pathways.

Deep learning techniques for energy clustering in the CMS electromagnetic calorimeter

The reconstruction of electrons and photons in CMS depends on the topological clustering of the energy deposited by an incident particle in different crystals of the electromagnetic calorimeter (ECAL). The currently used algorithm cannot account for the energy deposits coming from the pileup (secondary collisions) efficiently. The performance of this algorithm is expected to degrade during the LHC Run 3 because of the larger average pileup level and the increasing level of noise due to the aging of the ECAL detector. In this paper, we explore new techniques for energy reconstruction in ECAL using state-of-the-art machine learning algorithms like graph neural networks and self-attention modules.

The synaptic organization in the Caenorhabditis elegans neural network suggests significant local compartmentalized computations

Neurons are characterized by elaborate tree-like dendritic structures that support local computations by integrating multiple inputs from upstream presynaptic neurons. It is less clear whether simple neurons, consisting of a few or even a single neurite, may perform local computations as well. To address this question, we focused on the compact neural network of Caenorhabditis elegansanimals for which the full wiring diagram is available, including the coordinates of individual synapses. We find that the positions of the chemical synapses along the neurites are not randomly distributed nor can they be explained by anatomical constraints. Instead, synapses tend to form clusters, an organization that supports local compartmentalized computations. In mutually synapsing neurons, connections of opposite polarity cluster separately, suggesting that positive and negative feedback dynamics may be implemented in discrete compartmentalized regions along neurites. In triple-neuron circuits, the nonrandom synaptic organization may facilitate local functional roles, such as signal integration and coordinated activation of functionally related downstream neurons. These clustered synaptic topologies emerge as a guiding principle in the network, presumably to facilitate distinct parallel functions along a single neurite, which effectively increase the computational capacity of the neural network.

SPCIM: Sparsity-Balanced Practical CIM Accelerator With Optimized Spatial-Temporal Multi-Macro Utilization

Compute-in-memory (CIM) is a promising technique that reduces data movement in neural network (NN) acceleration. To achieve higher efficiency, some recent CIM accelerators exploit NN sparsity based on CIM’s small-grained operation unit (OU) feature. However, new problems arise in a practical multi-macro accelerator: The mismatch between workload parallelism and CIM macro organization causes spatial under-utilization; The multiple macros’ different computation time leads to temporal under-utilization. To solve the under-utilization problems, we propose a Sparsity-balanced Practical CIM accelerator (SPCIM), including optimized dataflow and hardware architecture design. For the CIM dataflow design, we first propose a reconfigurable cluster topology for CIM macro organization. Then we regularize weight sparsity in the OU-height pattern and reorder the weight matrix based on the sparsity ratio. The cluster topology can be reshaped to match workload parallelism for higher spatial utilization. Each CIM cluster’s workload is dynamically rebalanced for higher temporal utilization. Our hardware architecture supports the proposed dataflow with a spatial input dispatcher and a temporal workload allocator. Experimental results show that, compared with the baseline sparse CIM accelerator that suffers from spatial and temporal under-utilization, SPCIM achieves <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2.94\times $ </tex-math></inline-formula> speedup and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$2.86\times $ </tex-math></inline-formula> energy saving. The proposed sparsity-balanced dataflow and architecture are generic and scalable, which can be applied to other CIM accelerators. We strengthen two state-of-the-art CIM accelerators with the SPCIM techniques, improving their energy efficiency by <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$1.92\times $ </tex-math></inline-formula> and <inline-formula xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink"> <tex-math notation="LaTeX">$5.59\times $ </tex-math></inline-formula> , respectively.

Differential membrane curvature induced by distinct protein conformers.

Membrane topology changes are associated with various cellular processes and are modulated by synergistic effects between lipid composition and membrane-associated proteins. However, how protein shape or conformational dynamics couples to membrane molecular properties remains unclear. In this work, we aim to investigate this coupling behavior using the curvature-inducing protein caveolin-1. We considered distinct protein conformers of the helical hairpin protein corresponding to different protein shapes, such as the wedge and the banana-shaped conformers. The different protein conformers were simulated in a coarse-grain representation in the presence of cholesterol-sphingomyelin rich membrane. We observed that membrane curvature is dependent on protein shape and is the lowest for the wedge conformer and maximal for the banana conformer. The differences in the net stress between the two membrane leaflets, calculated from the lateral pressure profile distributions in lipid bilayers for different protein conformers, show a similar trend. In conjunction, we show that cholesterol and sphingomyelin clustering in the membrane is modulated by protein shape. Overall, our results provide molecular-level insights into the coupling between membrane topology, protein shape and lipid clustering in cell membranes.

The Mechanism of Quercetin in the Treatment of Lung Squamous Cell Carcinoma Based on a Protein-Protein Interaction Network.

Lung squamous cell carcinoma (LUSC) is characterized by poor prognosis and obvious limitations of therapeutic methods. The molecular target and mechanism of quercetin (QR), a natural anticancer product with extensive pharmacological activities, on lung squamous cell carcinoma is still unclear. The effects of QR on LUSC were examined using cell proliferation, migration, and invasion tests. Key target genes were screened using The Cancer Genome Atlas (TCGA) database, Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG) database, STRING website, topology, and prognosis analysis, molecular docking, and other bioinformatics methods for further analysis. Finally, the effects of QR on the expression of key targets in LUSC cells were detected using a cell cycle assay and western blotting. Our study demonstrates that QR not only inhibits the proliferation of LUSC but also affects the invasion and metastasis of LUSC. After downloading and analyzing the TCGA database, 2150 differentially expressed genes were identified. PLK1, CDC20, and BUB1B were identified using enrichment analysis, topological network analysis, cluster analysis, and molecular docking screening. Subsequent experiments showed that QR could interfere with the cell cycle and downregulate the expression of the target gene PLK1 at the protein level. We found that QR not only inhibits the proliferation, migration, and invasion but also blocks the cell cycle progression of LUSC. QR downregulated the expression of the LUSC target gene PLK1 at the protein level.

Deep reinforcement learning based topology-aware voltage regulation of distribution networks with distributed energy storage

Both the high penetration of clean energy with strong fluctuation and the complicated variable operation condition bring great challenges to the voltage regulation of the distribution network. To deal with the problem, a topology-aware voltage regulation multi-agent deep reinforcement learning (MADRL) algorithm is proposed. The distributed energy storages (DESs) are modeled as agents to regulate voltage autonomously in real-time, which could fast adapt to dynamic topological scenarios. Firstly, taking the minimization of voltage fluctuation and maximization of reserve capacity as the target, the optimal voltage regulation model is established. Secondly, a topology extraction method considering voltage sensitivity is proposed for dynamic topology clustering, and the obtained typical topology is added to the observation set of agents. Then, the optimal voltage regulation model is formulated to the decentralized partially observable Markov decision process (Dec-POMDP) framework, in which only local information is required for the agent during the test process to decision-making to realize the hierarchical and partitioned control of voltage. Finally, the multi-agent deep deterministic policy gradient (MADDPG) algorithm is used to solve the Dec-POMDP model. The feasibility and superiority of the proposed algorithm are verified and analyzed in the simulation under different scenarios.

RANCE: A Randomly Centralized and On-Demand Clustering Protocol for Mobile Ad Hoc Networks

LEACH-like clustering protocols focus mainly on the low-power, low-rate, and low-wakeup network applications, and work in a multiround clustering strategy that causes frequent handovers of cluster heads (CHs), thus less support for real-time services that require stable cluster topologies. Besides, these protocols are faced with respective drawbacks, such as suboptimality of selected heads, costly node-base station (BS) energy overheads, lack of runtime cluster maintenance, etc. This article proposes RANCE, a randomly centralized and on-demand clustering protocol, aiming at prolonging nodes’ clustered time to support internodes collaboration while being energy efficient in mobile ad hoc networks. First, RANCE designs a randomly centralized CH selection mechanism in which every node in the local wireless network is eligible to initiate the centralized CH selection, so that the self-organizing characteristics of mobile ad hoc nodes can be utilized for head selection optimization. Second, taking into account the wireless volatility caused by changes of topology, obstacles, signal strength, etc., the fine-grained cluster relationships maintenance is provided by means of multilevel aliveness and adaptive bidirectional heartbeat packets. Third, RANCE works in an event-driven and on-demand manner instead of a time-triggered manner in LEACH-like protocols, to reduce the impact on continuous services caused by frequent CH handovers among all nodes. Simulation results show that RANCE provides longer clustered time (over 99% of nodes’ lifetime in networks more than 100 nodes) and good clustering scalability with high consistency at minimum energy cost, and exhibits good potentials in mobile wireless environments that are infrastructureless/poor for continuous missions.