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1. TAXOGAN: Hierarchical Network Representation Learning via Taxonomy Guided Generative Adversarial Networks (Extended Abstract)

   https://doi.org/10.24963/ijcai.2021/666  

   Yang, Carl; Zhang, Jieyu; Han, Jiawei (August 2021, IJCAI'21 Proc. 13th International Joint Conference on Artificial Intelligence)

   Zhi (Ed.)

   Network representation learning aims at transferring node proximity in networks into distributed vectors, which can be leveraged in various downstream applications. Recent research has shown that nodes in a network can often be organized in latent hierarchical structures, but without a particular underlying taxonomy, the learned node embedding is less useful nor interpretable. In this work, we aim to improve network embedding by modeling the conditional node proximity in networks indicated by node labels residing in real taxonomies. In the meantime, we also aim to model the hierarchical label proximity in the given taxonomies, which is too coarse by solely looking at the hierarchical topologies. Comprehensive experiments and case studies demonstrate the utility of TAXOGAN. 

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2. Toward Understanding and Evaluating Structural Node Embeddings

   https://doi.org/10.1145/3481639  

   Jin, Junchen; Heimann, Mark; Jin, Di; Koutra, Danai (June 2022, ACM Transactions on Knowledge Discovery from Data)

   While most network embedding techniques model the proximity between nodes in a network, recently there has been significant interest in structural embeddings that are based on node equivalences , a notion rooted in sociology: equivalences or positions are collections of nodes that have similar roles—i.e., similar functions, ties or interactions with nodes in other positions—irrespective of their distance or reachability in the network. Unlike the proximity-based methods that are rigorously evaluated in the literature, the evaluation of structural embeddings is less mature. It relies on small synthetic or real networks with labels that are not perfectly defined, and its connection to sociological equivalences has hitherto been vague and tenuous. With new node embedding methods being developed at a breakneck pace, proper evaluation, and systematic characterization of existing approaches will be essential to progress. To fill in this gap, we set out to understand what types of equivalences structural embeddings capture. We are the first to contribute rigorous intrinsic and extrinsic evaluation methodology for structural embeddings, along with carefully-designed, diverse datasets of varying sizes. We observe a number of different evaluation variables that can lead to different results (e.g., choice of similarity measure, classifier, and label definitions). We find that degree distributions within nodes’ local neighborhoods can lead to simple yet effective baselines in their own right and guide the future development of structural embedding. We hope that our findings can influence the design of further node embedding methods and also pave the way for more comprehensive and fair evaluation of structural embedding methods. 

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3. BI‐LAVA: Biocuration With Hierarchical Image Labelling Through Active Learning and Visual Analytics

   https://doi.org/10.1111/cgf.15261  

   Trelles, Juan; Wentzel, Andrew; Berrios, William; Shatkay, Hagit; Marai, G Elisabeta (February 2025, Computer Graphics Forum)

   Abstract In the biomedical domain, taxonomies organize the acquisition modalities of scientific images in hierarchical structures. Such taxonomies leverage large sets of correct image labels and provide essential information about the importance of a scientific publication, which could then be used in biocuration tasks. However, the hierarchical nature of the labels, the overhead of processing images, the absence or incompleteness of labelled data and the expertise required to label this type of data impede the creation of useful datasets for biocuration. From a multi‐year collaboration with biocurators and text‐mining researchers, we derive an iterative visual analytics and active learning (AL) strategy to address these challenges. We implement this strategy in a system called BI‐LAVA—Biocuration with Hierarchical Image Labelling through Active Learning and Visual Analytics. BI‐LAVA leverages a small set of image labels, a hierarchical set of image classifiers and AL to help model builders deal with incomplete ground‐truth labels, target a hierarchical taxonomy of image modalities and classify a large pool of unlabelled images. BI‐LAVA's front end uses custom encodings to represent data distributions, taxonomies, image projections and neighbourhoods of image thumbnails, which help model builders explore an unfamiliar image dataset and taxonomy and correct and generate labels. An evaluation with machine learning practitioners shows that our mixed human–machine approach successfully supports domain experts in understanding the characteristics of classes within the taxonomy, as well as validating and improving data quality in labelled and unlabelled collections. 

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4. TaxoGen: Unsupervised Topic Taxonomy Construction by Adaptive Term Embedding and Clustering

   https://doi.org/10.1145/3219819.3220064  

   Zhang, Chao; Tao, Fangbo; Chen, Xiusi; Shen, Jiaming; Jiang, Meng; Sadler, Brian; Vanni, Michelle; Han, Jiawei (August 2018, Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining, KDD 2018)

   Taxonomy construction is not only a fundamental task for semantic analysis of text corpora, but also an important step for applications such as information filtering, recommendation, and Web search. Existing pattern-based methods extract hypernym-hyponym term pairs and then organize these pairs into a taxonomy. However, by considering each term as an independent concept node, they overlook the topical proximity and the semantic correlations among terms. In this paper, we propose a method for constructing topic taxonomies, wherein every node represents a conceptual topic and is defined as a cluster of semantically coherent concept terms. Our method, TaxoGen, uses term embeddings and hierarchical clustering to construct a topic taxonomy in a recursive fashion. To ensure the quality of the recursive process, it consists of: (1) an adaptive spherical clustering module for allocating terms to proper levels when splitting a coarse topic into fine-grained ones; (2) a local embedding module for learning term embeddings that maintain strong discriminative power at different levels of the taxonomy. Our experiments on two real datasets demonstrate the effectiveness of TaxoGen compared with baseline methods. 

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5. SINE: Scalable Incomplete Network Embedding

   https://doi.org/10.1109/ICDM.2018.00089  

   Zhang, Daokun; Yin, Jie; Zhu, Xingquan; Zhang, Chengqi (November 2018, Proc. of the 18th IEEE International Conference on Data Mining (ICDM-2018))

   Attributed network embedding aims to learn lowdimensional vector representations for nodes in a network, where each node contains rich attributes/features describing node content. Because network topology structure and node attributes often exhibit high correlation, incorporating node attribute proximity into network embedding is beneficial for learning good vector representations. In reality, large-scale networks often have incomplete/missing node content or linkages, yet existing attributed network embedding algorithms all operate under the assumption that networks are complete. Thus, their performance is vulnerable to missing data and suffers from poor scalability. In this paper, we propose a Scalable Incomplete Network Embedding (SINE) algorithm for learning node representations from incomplete graphs. SINE formulates a probabilistic learning framework that separately models pairs of node-context and node-attribute relationships. Different from existing attributed network embedding algorithms, SINE provides greater flexibility to make the best of useful information and mitigate negative effects of missing information on representation learning. A stochastic gradient descent based online algorithm is derived to learn node representations, allowing SINE to scale up to large-scale networks with high learning efficiency. We evaluate the effectiveness and efficiency of SINE through extensive experiments on real-world networks. Experimental results confirm that SINE outperforms state-of-the-art baselines in various tasks, including node classification, node clustering, and link prediction, under settings with missing links and node attributes. SINE is also shown to be scalable and efficient on large-scale networks with millions of nodes/edges and high-dimensional node features. 

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