MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenome-assembled genomes

We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is capable of classifying large and diverse metagenomic datasets: a total of 245.68 Gbp in the training sets, and 9.6 Gbp in the test sets analyzed in this study. MT-MAG is, to the best of our knowledge, the first machine learning method for taxonomic assignment of metagenomic data that offers a “partial classification” option, whereby a classification at a higher taxonomic level is provided for MAGs that cannot be classified to the Species level. MT-MAG outputs complete or partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. To assess the performance of MT-MAG, we define a “weighted classification accuracy,” with a weighting scheme reflecting the fact that partial classifications at different ranks are not equally informative. For the two benchmarking datasets analyzed (genomes from human gut microbiome species, and bacterial and archaeal genomes assembled from cow rumen metagenomic sequences), MT-MAG achieves an average of 80.13% in weighted classification accuracy. At the Species level, MT-MAG outperforms DeepMicrobes, the only other comparable software tool, by an average of 35.75% in weighted classification accuracy. In addition, MT-MAG is able to completely classify an average of 67.7% of the sequences at the Species level, compared with DeepMicrobes which only classifies 47.45%. Moreover, MT-MAG provides additional information for sequences that it could not classify at the Species level, resulting in the partial or complete classification of 95.15%, of the genomes in the datasets analyzed. Lastly, unlike other taxonomic assignment tools (e.g., GDTB-Tk), MT-MAG is an alignment-free and genetic marker-free tool, able to provide additional bioinformatics analysis to confirm existing or tentative taxonomic assignments

First Language Loss and Maintenance in Adolescents and Young Adults from Immigrant Backgrounds

Abstract Language attrition is a documented phenomenon that occurs when individuals progressively lose their first language (Schmid et al., 2007). This is particularly common among individuals who relocate to a country that speaks a foreign language that differs from their first language, as the societal language eventually becomes their dominant language. Deterioration and loss of the first language (L1) may result in consequences such as loss of ethnic and cultural identity, leading to the loss of a link to one’s country of origin (Cho & Krashen, 1998). Thus, the present study examined factors that may contribute to L1 attrition. The present study aimed to assess individuals’ L1 skills in relation to their cultural affiliation with their heritage and/or Canadian backgrounds after the participants emigrated from their home country to a foreign country (Canada). This study also looked at whether participants’ L1 skills are preserved if they are residing in a multigenerational household. Participants were instructed to complete a series of surveys that measured their receptive vocabulary size in English, levels of acculturation to the host culture, and language dominance. Participants were also scheduled for a one-on-one Zoom session to assess their verbal fluency in their L1 and English. Group comparisons based on age of arrival and being born in Canada showed differences in self-reports of L1 and L2 skills, enculturation and acculturation. Group differences were also found for groups based on whether or not participants attended school only in Canada or also in another country. Also group differences were found based on differences in language dominance as measured by the bilingual dominance scale. However, no effect was found for participants who lived in a multi-generational home and those who did not. This exploratory study may provide insight into the field of language development and literacy by showing a comprehensive relationship between L1 loss and acculturation

Electric field enhancement of pool boiling of dielectric fluids on pillar-structured surfaces: A lattice Boltzmann study

In this paper, by using a phase-change lattice Boltzmann (LB) model coupled with an electric field model, we numerically investigate the performance and enhancement mechanism of pool boiling of dielectric fluids on pillar-structured surfaces under an electric field. The numerical investigation reveals that applying an electric field causes both positive and negative influences on the pool boiling of dielectric fluids on pillar-structured surfaces. It is found that, under the action of an electric field, the electric force prevents the bubbles nucleated in the channels from crossing the edges of the pillar tops. On the one hand, such an effect results in the bubble coalescence in the channels and blocks the paths of liquid supply for the channels, which leads to the deterioration of pool boiling in the medium-superheat regime. On the other hand, it prevents the coalescence between the bubbles in the channels and those on the pillar tops, which suppresses the formation of a continuous vapor film and therefore delays the occurrence of boiling crisis. Meanwhile, the electric force can promote the departure of the bubbles on the pillar tops. Accordingly, the critical heat flux (CHF) can be improved. Based on the revealed mechanism, wettability-modified regions are applied to the pillar tops for further enhancing the boiling heat transfer. It is shown that the boiling performance on pillar-structured surfaces can be enhanced synergistically with the CHF being increased by imposing an electric field and the maximum heat transfer coefficient being improved by applying mixed wettability to the pillar-structured surfaces.Comment: 29 pages, 16 figure

A Hierarchical and Location-aware Consensus Protocol for IoT-Blockchain Applications

Blockchain-based IoT systems can manage IoT devices and achieve a high level of data integrity, security, and provenance. However, incorporating existing consensus protocols in many IoT systems limits scalability and leads to high computational cost and consensus latency. In addition, location-centric characteristics of many IoT applications paired with limited storage and computing power of IoT devices bring about more limitations, primarily due to the location-agnostic designs in blockchains. We propose a hierarchical and location-aware consensus protocol (LH-Raft) for IoT-blockchain applications inspired by the original Raft protocol to address these limitations. The proposed LH-Raft protocol forms local consensus candidate groups based on nodes' reputation and distance to elect the leaders in each sub-layer blockchain. It utilizes a threshold signature scheme to reach global consensus and the local and global log replication to maintain consistency for blockchain transactions. To evaluate the performance of LH-Raft, we first conduct an extensive numerical analysis based on the proposed reputation mechanism and the candidate group formation model. We then compare the performance of LH-Raft against the classical Raft protocol from both theoretical and experimental perspectives. We evaluate the proposed threshold signature scheme using Hyperledger Ursa cryptography library to measure various consensus nodes' signing and verification time. Experimental results show that the proposed LH-Raft protocol is scalable for large IoT applications and significantly reduces the communication cost, consensus latency, and agreement time for consensus processing.Comment: Published in IEEE Transactions on Network and Service Management ( Volume: 19, Issue: 3, September 2022). arXiv admin note: text overlap with arXiv:2305.1696

Traffic Prediction using Artificial Intelligence: Review of Recent Advances and Emerging Opportunities

Traffic prediction plays a crucial role in alleviating traffic congestion which represents a critical problem globally, resulting in negative consequences such as lost hours of additional travel time and increased fuel consumption. Integrating emerging technologies into transportation systems provides opportunities for improving traffic prediction significantly and brings about new research problems. In order to lay the foundation for understanding the open research challenges in traffic prediction, this survey aims to provide a comprehensive overview of traffic prediction methodologies. Specifically, we focus on the recent advances and emerging research opportunities in Artificial Intelligence (AI)-based traffic prediction methods, due to their recent success and potential in traffic prediction, with an emphasis on multivariate traffic time series modeling. We first provide a list and explanation of the various data types and resources used in the literature. Next, the essential data preprocessing methods within the traffic prediction context are categorized, and the prediction methods and applications are subsequently summarized. Lastly, we present primary research challenges in traffic prediction and discuss some directions for future research.Comment: Published in Transportation Research Part C: Emerging Technologies (TR_C), Volume 145, 202

B^2SFL: A Bi-level Blockchained Architecture for Secure Federated Learning-based Traffic Prediction

Federated Learning (FL) is a privacy-preserving machine learning (ML) technology that enables collaborative training and learning of a global ML model based on aggregating distributed local model updates. However, security and privacy guarantees could be compromised due to malicious participants and the centralized FL server. This article proposed a bi-level blockchained architecture for secure federated learning-based traffic prediction. The bottom and top layer blockchain store the local model and global aggregated parameters accordingly, and the distributed homomorphic-encrypted federated averaging (DHFA) scheme addresses the secure computation problems. We propose the partial private key distribution protocol and a partially homomorphic encryption/decryption scheme to achieve the distributed privacy-preserving federated averaging model. We conduct extensive experiments to measure the running time of DHFA operations, quantify the read and write performance of the blockchain network, and elucidate the impacts of varying regional group sizes and model complexities on the resulting prediction accuracy for the online traffic flow prediction task. The results indicate that the proposed system can facilitate secure and decentralized federated learning for real-world traffic prediction tasks.Comment: Paper accepted for publication in IEEE Transactions on Services Computing (TSC

BFRT: Blockchained Federated Learning for Real-time Traffic Flow Prediction

Accurate real-time traffic flow prediction can be leveraged to relieve traffic congestion and associated negative impacts. The existing centralized deep learning methodologies have demonstrated high prediction accuracy, but suffer from privacy concerns due to the sensitive nature of transportation data. Moreover, the emerging literature on traffic prediction by distributed learning approaches, including federated learning, primarily focuses on offline learning. This paper proposes BFRT, a blockchained federated learning architecture for online traffic flow prediction using real-time data and edge computing. The proposed approach provides privacy for the underlying data, while enabling decentralized model training in real-time at the Internet of Vehicles edge. We federate GRU and LSTM models and conduct extensive experiments with dynamically collected arterial traffic data shards. We prototype the proposed permissioned blockchain network on Hyperledger Fabric and perform extensive tests using virtual machines to simulate the edge nodes. Experimental results outperform the centralized models, highlighting the feasibility of our approach for facilitating privacy-preserving and decentralized real-time traffic flow prediction.Comment: Published in 2022 22nd IEEE International Symposium on Cluster, Cloud and Internet Computing (CCGrid