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Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.

 

Multi-layered inter-dependent networks have emerged in a wealth of high-impact application domains. Cross-layer dependency inference, which aims to predict the dependencies between nodes across different layers, plays a pivotal role in such multi-layered network systems. Most, if not all, of existing methods exclusively follow a coupling principle of design and can be categorized into the following two groups, including (1) heterogeneous network embedding based methods (data coupling), and (2) collaborative filtering based methods (module coupling). Despite the favorable achievement, methods of both types are faced with two intricate challenges, including (1) the sparsity challenge where very limited observations of cross-layer dependencies are available, resulting in a deteriorated prediction of missing dependencies, and (2) the dynamic challenge given that the multi-layered network system is constantly evolving over time. In this paper, we first demonstrate that the inability of existing methods to resolve the sparsity challenge roots in the coupling principle from the perspectives of both data coupling and module coupling. Armed with such theoretical analysis, we pursue a new principle where the key idea is to decouple the within-layer connectivity from the observed cross-layer dependencies. Specifically, to tackle the sparsity challenge for static networks, we propose FITO-S, which incorporates a position embedding matrix generated by random walk with restart and the embedding space transformation function. More essentially, the decoupling principle ameliorates the dynamic challenge, which naturally leads to FITO-D, being capable of tracking the inference results in the dynamic setting through incrementally updating the position embedding matrix and fine-tuning the space transformation function. Extensive evaluations on real-world datasets demonstrate the superiority of the proposed framework FITO for cross-layer dependency inference. 

Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.

 

Knowledge graph (KG for short) alignment aims at building a complete KG by linking the shared entities across complementary KGs. Existing approaches assume that KGs are static, despite the fact that almost every KG evolves over time. In this paper, we introduce the task of dynamic knowledge graph alignment, the main challenge of which is how to efficiently update entity embeddings for the evolving graph topology. Our key insight is to view the parameter matrix of GCN as a feature transformation operator and decouple the transformation process from the aggregation process. Based on that, we first propose a novel base algorithm (DINGAL-B) with topology-invariant mask gate and highway gate, which consistently outperforms 14 existing knowledge graph alignment methods in the static setting. More importantly, it naturally leads to two effective and efficient algorithms to align dynamic knowledge graph, including (1) DINGAL-O which leverages previous parameter matrices to update the embeddings of affected entities; and (2) DINGAL-U which resorts to newly obtained anchor links to fine-tune parameter matrices. Compared with their static counterpart (DINGAL-B), DINGAL-U and DINGAL-O are 10× and 100× faster respectively, with little alignment accuracy loss. 

Networks (i.e., graphs) are often collected from multiple sources and platforms, such as social networks extracted from multiple online platforms, team-specific collaboration networks within an organization, and inter-dependent infrastructure networks, etc. Such networks from different sources form the multi-networks, which can exhibit the unique patterns that are invisible if we mine the individual network separately. However, compared with single-network mining, multi-network mining is still under-explored due to its unique challenges. First ( multi-network models ), networks under different circumstances can be modeled into a variety of models. How to properly build multi-network models from the complex data? Second ( multi-network mining algorithms ), it is often nontrivial to either extend single-network mining algorithms to multi-networks or design new algorithms. How to develop effective and efficient mining algorithms on multi-networks? The objectives of this tutorial are to: (1) comprehensively review the existing multi-network models, (2) elaborate the techniques in multi-network mining with a special focus on recent advances, and (3) elucidate open challenges and future research directions. We believe this tutorial could be beneficial to various application domains, and attract researchers and practitioners from data mining as well as other interdisciplinary fields.