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Energy load balancing is an essential issue in designing wireless sensor networks (WSNs). Clustering techniques are utilized as energy-efficient methods to balance the network energy and prolong its lifetime. In this paper, we propose an improved soft-k-means (IS-k-means) clustering algorithm to balance the energy consumption of nodes in WSNs. First, we use the idea of ``clustering by fast search and find of density peaks'' (CFSFDP) and kernel density estimation (KDE) to improve the selection of the initial cluster centers of the soft k-means clustering algorithm. Then, we utilize the flexibility of the soft-k-means and reassign member nodes considering their membership probabilities at the boundary of clusters to balance the number of nodes per cluster. Furthermore, the concept of multi-cluster heads is employed to balance the energy consumption within clusters. {Extensive simulation results under different network scenarios demonstrate that for small-scale WSNs with single-hop transmission}, the proposed algorithm can postpone the first node death, the half of nodes death, and the last node death on average when compared to various clustering algorithms from the literature.

Maintaining freshness of data collection in Internet-of-Things (IoT) networks has attracted increasing attention. By taking into account age-of-information (AoI), we investigate the trajectory planning problem of an unmanned aerial vehicle (UAV) that is used to aid a cluster-based IoT network. An optimization problem is formulated to minimize the total AoI of the collected data by the UAV from the ground IoT network. Since the total AoI of the IoT network depends on the flight time of the UAV and the data collection time at hovering points, we jointly optimize the selection of hovering points and the visiting order to these points. We exploit the state-of-the-art transformer and the weighted A*, which is a path search algorithm, to design a machine learning algorithm to solve the formulated problem. The whole UAV-IoT system is fed into the encoder network of the proposed algorithm, and the algorithm's decoder network outputs the visiting order to ground clusters. Then, the weighted A* is used to find the hovering point for each cluster in the ground IoT network. Simulation results show that the trained model by the proposed algorithm has a good generalization ability to generate solutions for IoT networks with different numbers of ground clusters, without the need to retrain the model. Furthermore, results show that our proposed algorithm can find better UAV trajectories with the minimum total AoI when compared to other algorithms.

Chirps spread spectrum (CSS) modulation is the heart of long-range (LoRa) modulation used in the context of long-range wide area network (LoRaWAN) in internet of things (IoT) scenarios. Despite being a proprietary technology owned by Semtech Corp., LoRa modulation has drawn much attention from the research and industry communities in recent years. However, to the best of our knowledge, a comprehensive tutorial, investigating the CSS modulation in the LoRaWAN application, is missing in the literature. Therefore, in the first part of this paper, we provide a thorough analysis and tutorial of CSS modulation modified by LoRa specifications, discussing various aspects such as signal generation, detection, error performance, and spectral characteristics. Moreover, a summary of key recent advances in the context of CSS modulation applications in IoT networks is presented in the second part of this paper under four main categories of transceiver configuration and design, data rate improvement, interference modeling, and synchronization algorithms., Comment: This work is under review in IEEE Communications Surveys and Tutorials

This paper proposes a novel design of multi-symbol unitary constellation for non-coherent single-input multiple-output (SIMO) communications over block Rayleigh fading channels. To facilitate the design and the detection of large unitary constellations at reduced complexity, the proposed constellations are constructed as the Cartesian product of independent amplitude and phase-shift-keying (PSK) vectors, and hence, can be iteratively detected. The amplitude vector is detected by exhaustive search, whose complexity is sufficiently low in short packet transmission scenarios. To detect the PSK vector, we use the posterior probability as a reliability criterion in the sorted decision-feedback differential detection (sort-DFDD), which results in near-optimal error performance for PSK symbols with equal modulation orders. This detector is called posteriori-based-reliability-sort-DFDD (PR-sort-DFDD) and has polynomial complexity. We also propose an improved detector called improved-PR-sort-DFDD to detect a more generalized PSK structure, i.e., PSK symbols with unequal modulation orders. This detector also approaches the optimal error performance with polynomial complexity. Simulation results show the merits of our proposed multi-symbol unitary constellation when compared to competing low-complexity unitary constellations., Comment: 13 pages, 10 figures, in preparation to submit to IEEE Transactions on Wireless Communications

In this paper, we present a device-to-device (D2D) transmission scheme for aiding long-range frequency hopping spread spectrum (LR-FHSS) LoRaWAN protocol with application in direct-to-satellite IoT networks. We consider a practical ground-to-satellite fading model, i.e. shadowed-Rice channel, and derive the outage performance of the LR-FHSS network. With the help of network coding, D2D-aided LR-FHSS transmission scheme is proposed to improve the network capacity for which a closed-form outage probability expression is also derived. The obtained analytical expressions for both LR-FHSS and D2D-aided LR-FHSS outage probabilities are validated by computer simulations for different parts of the analysis capturing the effects of noise, fading, unslotted ALOHA-based time scheduling, the receiver's capture effect, IoT device distributions, and distance from node to satellite. The total outage probability for the D2D-aided LR-FHSS shows a considerable increase of 249.9% and 150.1% in network capacity at a typical outage of 10^-2 for DR6 and DR5, respectively, when compared to LR-FHSS. This is obtained at the cost of minimum of one and maximum of two additional transmissions per each IoT end device imposed by the D2D scheme in each time-slot., Comment: This paper is unuder review in IEEE Internet of Things Journal

Predicting the responses of a cell under perturbations may bring important benefits to drug discovery and personalized therapeutics. In this work, we propose a novel graph variational Bayesian causal inference framework to predict a cell's gene expressions under counterfactual perturbations (perturbations that this cell did not factually receive), leveraging information representing biological knowledge in the form of gene regulatory networks (GRNs) to aid individualized cellular response predictions. Aiming at a data-adaptive GRN, we also developed an adjacency matrix updating technique for graph convolutional networks and used it to refine GRNs during pre-training, which generated more insights on gene relations and enhanced model performance. Additionally, we propose a robust estimator within our framework for the asymptotically efficient estimation of marginal perturbation effect, which is yet to be carried out in previous works. With extensive experiments, we exhibited the advantage of our approach over state-of-the-art deep learning models for individual response prediction.

Estimating an individual's potential outcomes under counterfactual treatments is a challenging task for traditional causal inference and supervised learning approaches when the outcome is high-dimensional (e.g. gene expressions, impulse responses, human faces) and covariates are relatively limited. In this case, to construct one's outcome under a counterfactual treatment, it is crucial to leverage individual information contained in its observed factual outcome on top of the covariates. We propose a deep variational Bayesian framework that rigorously integrates two main sources of information for outcome construction under a counterfactual treatment: one source is the individual features embedded in the high-dimensional factual outcome; the other source is the response distribution of similar subjects (subjects with the same covariates) that factually received this treatment of interest.

The problem of how to genetically modify cells in order to maximize a certain cellular phenotype has taken center stage in drug development over the last few years (with, for example, genetically edited CAR-T, CAR-NK, and CAR-NKT cells entering cancer clinical trials). Exhausting the search space for all possible genetic edits (perturbations) or combinations thereof is infeasible due to cost and experimental limitations. This work provides a theoretically sound framework for iteratively exploring the space of perturbations in pooled batches in order to maximize a target phenotype under an experimental budget. Inspired by this application domain, we study the problem of batch query bandit optimization and introduce the Optimistic Arm Elimination ($\mathrm{OAE}$) principle designed to find an almost optimal arm under different functional relationships between the queries (arms) and the outputs (rewards). We analyze the convergence properties of $\mathrm{OAE}$ by relating it to the Eluder dimension of the algorithm's function class and validate that $\mathrm{OAE}$ outperforms other strategies in finding optimal actions in experiments on simulated problems, public datasets well-studied in bandit contexts, and in genetic perturbation datasets when the regression model is a deep neural network. OAE also outperforms the benchmark algorithms in 3 of 4 datasets in the GeneDisco experimental planning challenge., Comment: 22 pages main, 15 pages appendix

Translating the relevance of preclinical models ($\textit{in vitro}$, animal models, or organoids) to their relevance in humans presents an important challenge during drug development. The rising abundance of single-cell genomic data from human tumors and tissue offers a new opportunity to optimize model systems by their similarity to targeted human cell types in disease. In this work, we introduce SystemMatch to assess the fit of preclinical model systems to an $\textit{in sapiens}$ target population and to recommend experimental changes to further optimize these systems. We demonstrate this through an application to developing $\textit{in vitro}$ systems to model human tumor-derived suppressive macrophages. We show with held-out $\textit{in vivo}$ controls that our pipeline successfully ranks macrophage subpopulations by their biological similarity to the target population, and apply this analysis to rank a series of 18 $\textit{in vitro}$ macrophage systems perturbed with a variety of cytokine stimulations. We extend this analysis to predict the behavior of 66 $\textit{in silico}$ model systems generated using a perturbational autoencoder and apply a $k$-medoids approach to recommend a subset of these model systems for further experimental development in order to fully explore the space of possible perturbations. Through this use case, we demonstrate a novel approach to model system development to generate a system more similar to human biology., Comment: Published at the MLDD workshop, ICLR 2022

Employing unmanned aerial vehicles (UAVs) has attracted growing interests and emerged as the state-of-the-art technology for data collection in Internet-of-Things (IoT) networks. In this paper, with the objective of minimizing the total energy consumption of the UAV-IoT system, we formulate the problem of jointly designing the UAV's trajectory and selecting cluster heads in the IoT network as a constrained combinatorial optimization problem which is classified as NP-hard and challenging to solve. We propose a novel deep reinforcement learning (DRL) with a sequential model strategy that can effectively learn the policy represented by a sequence-to-sequence neural network for the UAV's trajectory design in an unsupervised manner. Through extensive simulations, the obtained results show that the proposed DRL method can find the UAV's trajectory that requires much less energy consumption when compared to other baseline algorithms and achieves close-to-optimal performance. In addition, simulation results show that the trained model by our proposed DRL algorithm has an excellent generalization ability to larger problem sizes without the need to retrain the model., Comment: This paper has been accepted in IEEE IoT-J

Unmanned aerial vehicles (UAVs) have emerged as a promising candidate solution for data collection of large-scale wireless sensor networks (WSNs). In this paper, we investigate a UAV-aided WSN, where cluster heads (CHs) receive data from their member nodes, and a UAV is dispatched to collect data from CHs along the planned trajectory. We aim to minimize the total energy consumption of the UAV-WSN system in a complete round of data collection. Toward this end, we formulate the energy consumption minimization problem as a constrained combinatorial optimization problem by jointly selecting CHs from nodes within clusters and planning the UAV's visiting order to the selected CHs. The formulated energy consumption minimization problem is NP-hard, and hence, hard to solve optimally. In order to tackle this challenge, we propose a novel deep reinforcement learning (DRL) technique, pointer network-A* (Ptr-A*), which can efficiently learn from experiences the UAV trajectory policy for minimizing the energy consumption. The UAV's start point and the WSN with a set of pre-determined clusters are fed into the Ptr-A*, and the Ptr-A* outputs a group of CHs and the visiting order to these CHs, i.e., the UAV's trajectory. The parameters of the Ptr-A* are trained on small-scale clusters problem instances for faster training by using the actor-critic algorithm in an unsupervised manner. At inference, three search strategies are also proposed to improve the quality of solutions. Simulation results show that the trained models based on 20-clusters and 40-clusters have a good generalization ability to solve the UAV's trajectory planning problem in WSNs with different numbers of clusters, without the need to retrain the models. Furthermore, the results show that our proposed DRL algorithm outperforms two baseline techniques.

Despite the prevalence of hypergraphs in a variety of high-impact applications, there are relatively few works on hypergraph representation learning, most of which primarily focus on hyperlink prediction, often restricted to the transductive learning setting. Among others, a major hurdle for effective hypergraph representation learning lies in the label scarcity of nodes and/or hyperedges. To address this issue, this paper presents an end-to-end, bi-level pre-training strategy with Graph Neural Networks for hypergraphs. The proposed framework named HyperGene bears three distinctive advantages. First, it is capable of ingesting the labeling information when available, but more importantly, it is mainly designed in the self-supervised fashion which significantly broadens its applicability. Second, at the heart of the proposed HyperGene are two carefully designed pretexts, one on the node level and the other on the hyperedge level, which enable us to encode both the local and the global context in a mutually complementary way. Third, the proposed framework can work in both transductive and inductive settings. When applying the two proposed pretexts in tandem, it can accelerate the adaptation of the knowledge from the pre-trained model to downstream applications in the transductive setting, thanks to the bi-level nature of the proposed method. The extensive experimental results demonstrate that: (1) HyperGene achieves up to 5.69% improvements in hyperedge classification, and (2) improves pre-training efficiency by up to 42.80% on average.

Online stores often utilize product relationships such as bundles and substitutes to improve their catalog quality and guide customers through myriad choices. Entity resolution using pairwise product matching models offers a means of inferring relationships between products. In mature data repositories, the relationships may be mostly correct but require incremental improvements owing to errors in the original data or in the entity resolution system. It is critical to devise incremental entity resolution (IER) approaches for improving the health of relationships. However, most existing research on IER focuses on the addition of new products or information into existing relationships. Relatively little research has been done for detecting low quality within current relationships. This paper proposes a novel method for identifying inconsistent clusters (IC), existing groups of related products that do not belong together. We propose to treat the identification of inconsistent clusters as a supervised learning task which predicts whether a graph of products with similarities as weighted edges should be partitioned into multiple clusters. In this case, the problem becomes a classification task on weighted graphs and represents an interesting application area for modern tools such as Graph Neural Networks (GNNs). We demonstrate that existing Message Passing neural networks perform well at this task, exceeding traditional graph processing techniques. We also develop a novel message aggregation scheme for Message Passing Neural Networks that further improves the performance of GNNs on this task. We apply the model to synthetic datasets, a public benchmark dataset, and an internal application. Our results demonstrate the value of graph classification in IER and the ability of graph neural networks to develop useful representations for graph partitioning., Comment: Presented at the Knowledge Management for E-Commerce Workshop at WWW'21

High stress stoichiometric silicon nitride resonators, whose quality factors exceed one million, have shown promise for applications in sensing and signal processing. Yet, electrical integration of the insulating silicon nitride resonators has been challenging, as depositing even a thin layer of metal degrades the quality factor significantly. In this work, we show that graphene used as a conductive coating for Si3N4 membranes reduces the quality factor by less than 30 % on average, which is minimal when compared to the effect of conventional metallization layers such as chromium or aluminum. The electrical integration of Si3N4-Graphene (SiNG) heterostructure resonators is demonstrated with electrical readout and electro-static tuning of the frequency by up to 1 % per volt. These studies demonstrate the feasibility of hybrid graphene/nitride mechanical resonators in which the electrical properties of graphene are combined with the superior mechanical performance of silicon nitride., Comment: 8 pages, 5 figures, journal