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1. Heterformer: Transformer-based Deep Node Representation Learning on Heterogeneous Text-Rich Networks

   https://doi.org/10.1145/3580305.3599376  

   Jin, Bowen; Zhang, Yu; Zhu, Qi; Han, Jiawei (August 2023, ACM)

   Proc. 2023 ACM SIGKDD Int. Conf. on Knowledge Discovery and Data Mining (Ed.)

   Representation learning on networks aims to derive a meaningful vector representation for each node, thereby facilitating downstream tasks such as link prediction, node classification, and node clustering. In heterogeneous text-rich networks, this task is more challenging due to (1) presence or absence of text: Some nodes are associated with rich textual information, while others are not; (2) diversity of types: Nodes and edges of multiple types form a heterogeneous network structure. As pretrained language models (PLMs) have demonstrated their effectiveness in obtaining widely generalizable text representations, a substantial amount of effort has been made to incorporate PLMs into representation learning on text-rich networks. However, few of them can jointly consider heterogeneous structure (network) information as well as rich textual semantic information of each node effectively. In this paper, we propose Heterformer, a Heterogeneous Network-Empowered Transformer that performs contextualized text encoding and heterogeneous structure encoding in a unified model. Specifically, we inject heterogeneous structure information into each Transformer layer when encoding node texts. Meanwhile, Heterformer is capable of characterizing node/edge type heterogeneity and encoding nodes with or without texts. We conduct comprehensive experiments on three tasks (i.e., link prediction, node classification, and node clustering) on three large-scale datasets from different domains, where Heterformer outperforms competitive baselines significantly and consistently. 

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2. Learning Multimodal Representations for Unseen Activities

   https://doi.org/10.1109/WACV45572.2020.9093612  

   Piergiovanni, A.J.; Ryoo, Michael S. (March 2020, IEEE Winter Conference on Applications of Computer Vision (WACV))

   We present a method to learn a joint multimodal representation space that enables recognition of unseen activities in videos. We first compare the effect of placing various constraints on the embedding space using paired text and video data. We also propose a method to improve the joint embedding space using an adversarial formulation, allowing it to benefit from unpaired text and video data. By using unpaired text data, we show the ability to learn a representation that better captures unseen activities. In addition to testing on publicly available datasets, we introduce a new, large-scale text/video dataset. We experimentally confirm that using paired and unpaired data to learn a shared embedding space benefits three difficult tasks (i) zero-shot activity classification, (ii) unsupervised activity discovery, and (iii) unseen activity captioning, outperforming the state-of-the-arts. 

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3. Discriminative Topic Mining via Category-Name Guided Text Embedding

   https://doi.org/10.1145/3366423.3380278  

   Meng, Yu; Huang, Jiaxin; Wang, Guangyuan; Wang, Zihan; Zhang, Chao; Zhang, Yu; Han, Jiawei (April 2020, WWW '20: The Web Conference 2020)

   Mining a set of meaningful and distinctive topics automatically from massive text corpora has broad applications. Existing topic models, however, typically work in a purely unsupervised way, which often generate topics that do not fit users’ particular needs and yield suboptimal performance on downstream tasks. We propose a new task, discriminative topic mining, which leverages a set of user-provided category names to mine discriminative topics from text corpora. This new task not only helps a user understand clearly and distinctively the topics he/she is most interested in, but also benefits directly keyword-driven classification tasks. We develop CatE, a novel category-name guided text embedding method for discriminative topic mining, which effectively leverages minimal user guidance to learn a discriminative embedding space and discover category representative terms in an iterative manner. We conduct a comprehensive set of experiments to show that CatE mines highquality set of topics guided by category names only, and benefits a variety of downstream applications including weakly-supervised classification and lexical entailment direction identification. 

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4. ICoN: integration using co-attention across biological networks

   Tasnina, Nure; Murali, T M (November 2024, Bioinformatics advances)

   Motivation: Molecular interaction networks are powerful tools for studying cellular functions. Integrating diverse types of networks enhances performance in downstream tasks such as gene module detection and protein function prediction. The challenge lies in extracting meaningful protein feature representations due to varying levels of sparsity and noise across these heterogeneous networks. Results: We propose ICoN, a novel unsupervised graph neural network model that takes multiple protein–protein association networks as inputs and generates a feature representation for each protein that integrates the topological information from all the networks. A key contribution of ICoN is exploiting a mechanism called “co-attention” that enables cross-network communication during training. The model also incorporates a denoising training technique, introducing perturbations to each input network and training the model to reconstruct the original network from its corrupted version. Our experimental results demonstrate that ICoN surpasses individual networks across three downstream tasks: gene module detection, gene coannotation prediction, and protein function prediction. Compared to existing unsupervised network integration models, ICoN exhibits superior performance across the majority of downstream tasks and shows enhanced robustness against noise. This work introduces a promising approach for effectively integrating diverse protein–protein association networks, aiming to achieve a biologically meaningful representation of proteins. Availability and implementation: The ICoN software is available under the GNU Public License v3 at https://github.com/Murali-group/ICoN. 

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5. AND/OR Branch-and-Bound for Computational Protein Design Optimizing K*

   Pezeshki, Bobak; Marinescu, Radu; Ihler, Alexander; Dechter, Rina (January 2022, Proceedings of the 38th Conference on Uncertainty in Artificial Intelligence, PMLR)

   Cussens, James; Zhang, Kun (Ed.)

   The importance of designing proteins, such as high affinity antibodies, has become ever more apparent. Computational Protein Design can cast such design problems as optimization tasks with the objective of maximizing K*, an approximation of binding affinity. Here we lay out a graphical model framework for K* optimization that enables use of compact AND/OR search algorithms. We designed an AND/OR branch-and-bound algorithm, AOBB-K*, for optimizing K* that is guided by a new K* heuristic and can incorporate specialized performance improvements with theoretical guarantees. As AOBB-K* is inspired by algorithms from the well studied task of Marginal MAP, this work provides a foundation for harnessing advancements in state-of-the-art mixed inference schemes and adapting them to protein design. 

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