Hypergraph Neural Networks Reveal Spatial Domains from Single-cell Transcriptomics Data

The task of spatial clustering of transcriptomics data is of paramount importance. It enables the classification of tissue samples into diverse subpopulations of cells, which, in turn, facilitates the analysis of the biological functions of clusters, tissue reconstruction, and cell-cell interactions. Many approaches leverage gene expressions, spatial locations, and histological images to detect spatial domains; however, Graph Neural Networks (GNNs) as state of the art models suffer from a limitation in the assumption of pairwise connections between nodes. In the case of domain detection in spatial transcriptomics, some cells are found to be not directly related. Still, they are grouped as the same domain, which shows the incapability of GNNs for capturing implicit connections among the cells. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges, which lets Hypergraph Neural Networks (HGNNs) capture and utilize richer and more complex structural information than traditional GNNs. We use autoencoders to address the limitation of not having the actual labels, which are well-suited for unsupervised learning. Our model has demonstrated exceptional performance, achieving the highest iLISI score of 1.843 compared to other methods. This score indicates the greatest diversity of cell types identified by our method. Furthermore, our model outperforms other methods in downstream clustering, achieving the highest ARI values of 0.51 and Leiden score of 0.60.

Hyperedge Modeling in Hypergraph Neural Networks by using Densest Overlapping Subgraphs

Hypergraphs tackle the limitations of traditional graphs by introducing {\em hyperedges}. While graph edges connect only two nodes, hyperedges connect an arbitrary number of nodes along their edges. Also, the underlying message-passing mechanisms in Hypergraph Neural Networks (HGNNs) are in the form of vertex-hyperedge-vertex, which let HGNNs capture and utilize richer and more complex structural information than traditional Graph Neural Networks (GNNs). More recently, the idea of overlapping subgraphs has emerged. These subgraphs can capture more information about subgroups of vertices without limiting one vertex belonging to just one group, allowing vertices to belong to multiple groups or subgraphs. In addition, one of the most important problems in graph clustering is to find densest overlapping subgraphs (DOS). In this paper, we propose a solution to the DOS problem via Agglomerative Greedy Enumeration (DOSAGE) algorithm as a novel approach to enhance the process of generating the densest overlapping subgraphs and, hence, a robust construction of the hypergraphs. Experiments on standard benchmarks show that the DOSAGE algorithm significantly outperforms the HGNNs and six other methods on the node classification task.

Improving Out-of-Distribution Data Handling and Corruption Resistance via Modern Hopfield Networks

This study explores the potential of Modern Hopfield Networks (MHN) in improving the ability of computer vision models to handle out-of-distribution data. While current computer vision models can generalize to unseen samples from the same distribution, they are susceptible to minor perturbations such as blurring, which limits their effectiveness in real-world applications. We suggest integrating MHN into the baseline models to enhance their robustness. This integration can be implemented during the test time for any model and combined with any adversarial defense method. Our research shows that the proposed integration consistently improves model performance on the MNIST-C dataset, achieving a state-of-the-art increase of 13.84% in average corruption accuracy, a 57.49% decrease in mean Corruption Error (mCE), and a 60.61% decrease in relative mCE compared to the baseline model. Additionally, we investigate the capability of MHN to converge to the original non-corrupted data. Notably, our method does not require test-time adaptation or augmentation with corruptions, underscoring its practical viability for real-world deployment. (Source code publicly available at: https://github.com/salehsargolzaee/Hopfield-integrated-test)

Lusifer: LLM-based User SImulated Feedback Environment for online Recommender systems

Training reinforcement learning-based recommender systems are often hindered by the lack of dynamic and realistic user interactions. Lusifer, a novel environment leveraging Large Language Models (LLMs), addresses this limitation by generating simulated user feedback. It synthesizes user profiles and interaction histories to simulate responses and behaviors toward recommended items. In addition, user profiles are updated after each rating to reflect evolving user characteristics. Using the MovieLens100K dataset as proof of concept, Lusifer demonstrates accurate emulation of user behavior and preferences. This paper presents Lusifer's operational pipeline, including prompt generation and iterative user profile updates. While validating Lusifer's ability to produce realistic dynamic feedback, future research could utilize this environment to train reinforcement learning systems, offering a scalable and adjustable framework for user simulation in online recommender systems.