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1. End-to-end sequence-structure-function meta-learning predicts genome-wide chemical-protein interactions for dark proteins

   https://doi.org/10.1371/journal.pcbi.1010851  

   Cai, Tian ; Xie, Li ; Zhang, Shuo ; Chen, Muge ; He, Di ; Badkul, Amitesh ; Liu, Yang ; Namballa, Hari Krishna ; Dorogan, Michael ; Harding, Wayne W. ; et al ( January 2023 , PLOS Computational Biology)

   Skolnick, Jeffrey (Ed.)

   Systematically discovering protein-ligand interactions across the entire human and pathogen genomes is critical in chemical genomics, protein function prediction, drug discovery, and many other areas. However, more than 90% of gene families remain “dark”—i.e., their small-molecule ligands are undiscovered due to experimental limitations or human/historical biases. Existing computational approaches typically fail when the dark protein differs from those with known ligands. To address this challenge, we have developed a deep learning framework, called PortalCG, which consists of four novel components: (i) a 3-dimensional ligand binding site enhanced sequence pre-training strategy to encode the evolutionary links between ligand-binding sites across gene families; (ii) an end-to-end pretraining-fine-tuning strategy to reduce the impact of inaccuracy of predicted structures on function predictions by recognizing the sequence-structure-function paradigm; (iii) a new out-of-cluster meta-learning algorithm that extracts and accumulates information learned from predicting ligands of distinct gene families (meta-data) and applies the meta-data to a dark gene family; and (iv) a stress model selection step, using different gene families in the test data from those in the training and development data sets to facilitate model deployment in a real-world scenario. In extensive and rigorous benchmark experiments, PortalCG considerably outperformed state-of-the-art techniques of machine learning and protein-ligand docking when applied to dark gene families, and demonstrated its generalization power for target identifications and compound screenings under out-of-distribution (OOD) scenarios. Furthermore, in an external validation for the multi-target compound screening, the performance of PortalCG surpassed the rational design from medicinal chemists. Our results also suggest that a differentiable sequence-structure-function deep learning framework, where protein structural information serves as an intermediate layer, could be superior to conventional methodology where predicted protein structures were used for the compound screening. We applied PortalCG to two case studies to exemplify its potential in drug discovery: designing selective dual-antagonists of dopamine receptors for the treatment of opioid use disorder (OUD), and illuminating the understudied human genome for target diseases that do not yet have effective and safe therapeutics. Our results suggested that PortalCG is a viable solution to the OOD problem in exploring understudied regions of protein functional space. 

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2. Risk-Aware Resource Management in Public Safety Networks

   https://doi.org/10.3390/s19183853  

   Vamvakas, Panagiotis ; Tsiropoulou, Eirini Eleni ; Papavassiliou, Symeon ( September 2019 , Sensors)

   null (Ed.)

   Modern Public Safety Networks (PSNs) are assisted by Unmanned Aerial Vehicles (UAVs) to provide a resilient communication paradigm during catastrophic events. In this context, we propose a distributed user-centric risk-aware resource management framework in UAV-assisted PSNs supported by both a static UAV and a mobile UAV. The mobile UAV is entitled to a larger portion of the available spectrum due to its capability and flexibility to re-position itself, and therefore establish better communication channel conditions to the users, compared to the static UAV. However, the potential over-exploitation of the mobile UAV-based communication by the users may lead to the mobile UAV’s failure to serve the users due to the increased levels of interference, consequently introducing risk in the user decisions. To capture this uncertainty, we follow the principles of Prospect Theory and design a user’s prospect-theoretic utility function that reflects user’s risk-aware behavior regarding its transmission power investment to the static and/or mobile UAV-based communication option. A non-cooperative game among the users is formulated, where each user determines its power investment strategy to the two available communication choices in order to maximize its expected prospect-theoretic utility. The existence and uniqueness of a Pure Nash Equilibrium (PNE) is proven and the convergence of the users’ strategies to it is shown. An iterative distributed and low-complexity algorithm is introduced to determine the PNE. The performance of the proposed user-centric risk-aware resource management framework in terms of users’ achievable data rate and spectrum utilization, is achieved via modeling and simulation. Furthermore, its superiority and benefits are demonstrated, by comparing its performance against other existing approaches with regards to UAV selection and spectrum utilization. 

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3. Learning from Non-Experts: An Interactive and Adaptive Learning Approach for Appliance Recognition in Smart Homes

   https://doi.org/10.1145/3491241  

   Codispoti, Jackson ; Khamesi, Atieh R. ; Penn, Nelson ; Silvestri, Simone ; Shin, Eura ( February 2022 , ACM Transactions on Cyber-Physical Systems)

   With the acceleration of ICT technologies and the Internet of Things (IoT) paradigm, smart residential environments , also known as smart homes are becoming increasingly common. These environments have significant potential for the development of intelligent energy management systems, and have therefore attracted significant attention from both academia and industry. An enabling building block for these systems is the ability of obtaining energy consumption at the appliance-level. This information is usually inferred from electric signals data (e.g., current) collected by a smart meter or a smart outlet, a problem known as appliance recognition . Several previous approaches for appliance recognition have proposed load disaggregation techniques for smart meter data. However, these approaches are often very inaccurate for low consumption and multi-state appliances. Recently, Machine Learning (ML) techniques have been proposed for appliance recognition. These approaches are mainly based on passive MLs, thus requiring pre-labeled data to be trained. This makes such approaches unable to rapidly adapt to the constantly changing availability and heterogeneity of appliances on the market. In a home setting scenario, it is natural to consider the involvement of users in the labeling process, as appliances’ electric signatures are collected. This type of learning falls into the category of Stream-based Active Learning (SAL). SAL has been mainly investigated assuming the presence of an expert , always available and willing to label the collected samples. Nevertheless, a home user may lack such availability, and in general present a more erratic and user-dependent behavior. In this paper, we develop a SAL algorithm, called K -Active-Neighbors (KAN), for the problem of household appliance recognition. Differently from previous approaches, KAN jointly learns the user behavior and the appliance signatures. KAN dynamically adjusts the querying strategy to increase accuracy by considering the user availability as well as the quality of the collected signatures. Such quality is defined as a combination of informativeness , representativeness , and confidence score of the signature compared to the current knowledge. To test KAN versus state-of-the-art approaches, we use real appliance data collected by a low-cost Arduino-based smart outlet as well as the ECO smart home dataset. Furthermore, we use a real dataset to model user behavior. Results show that KAN is able to achieve high accuracy with minimal data, i.e., signatures of short length and collected at low frequency. 

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4. A Deep Reinforcement Learning-Based Resource Scheduler for Massive MIMO Networks

   Qing An ; Santiago Segarra ; Chris Dick ; Ashutosh Sabharwal ; Rahman Doost-Mohammady ( September 2023 , IEEE transactions on machine learning in communications and networking)

   The large number of antennas in massive MIMO systems allows the base station to communicate with multiple users at the same time and frequency resource with multi-user beamforming. However, highly correlated user channels could drastically impede the spectral efficiency that multi-user beamforming can achieve. As such, it is critical for the base station to schedule a suitable group of users in each time and frequency resource block to achieve maximum spectral efficiency while adhering to fairness constraints among the users. In this paper, we consider the resource scheduling problem for massive MIMO systems with its optimal solution known to be NP-hard. Inspired by recent achievements in deep reinforcement learning (DRL) to solve problems with large action sets, we propose SMART, a dynamic scheduler for massive MIMO based on the state-of-the-art Soft Actor-Critic (SAC) DRL model and the K-Nearest Neighbors (KNN) algorithm. Through comprehensive simulations using realistic massive MIMO channel models as well as real-world datasets from channel measurement experiments, we demonstrate the effectiveness of our proposed model in various channel conditions. Our results show that our proposed model performs very close to the optimal proportionally fair (Opt-PF) scheduler in terms of spectral efficiency and fairness with more than one order of magnitude lower computational complexity in medium network sizes where Opt-PF is computationally feasible. Our results also show the feasibility and high performance of our proposed scheduler in networks with a large number of users and resource blocks. 

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5. Analog Compression and Communication for Federated Learning over Wireless MAC

   https://doi.org/10.1109/SPAWC48557.2020.9154309  

   Abdi, Afshin ; Saidutta, Yashas Malur ; Fekri, Faramarz ( August 2020 , IEEE 21st International Workshop on Signal Processing Advances in Wireless Communications (SPAWC))

   null (Ed.)

   In this paper, we consider federated learning in wireless edge networks. Transmitting stochastic gradients (SG) or deep model's parameters over a limited-bandwidth wireless channel can incur large training latency and excessive power consumption. Hence, data compressing is often used to reduce the communication overhead. However, efficient communication requires the compression algorithm to satisfy the constraints imposed by the communication medium and take advantage of its characteristics, such as over-the-air computations inherent in wireless multiple-access channels (MAC), unreliable transmission and idle nodes in the edge network, limited transmission power, and preserving the privacy of data. To achieve these goals, we propose a novel framework based on Random Linear Coding (RLC) and develop efficient power management and channel usage techniques to manage the trade-offs between power consumption, communication bit-rate and convergence rate of federated learning over wireless MAC. We show that the proposed encoding/decoding results in an unbiased compression of SG, hence guaranteeing the convergence of the training algorithm without requiring error-feedback. Finally, through simulations, we show the superior performance of the proposed method over other existing techniques. 

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