PhenoProfiler: Advancing Phenotypic Learning for Image-based Drug Discovery

In the field of image-based drug discovery, capturing the phenotypic response of cells to various drug treatments and perturbations is a crucial step. However, existing methods require computationally extensive and complex multi-step procedures, which can introduce inefficiencies, limit generalizability, and increase potential errors. To address these challenges, we present PhenoProfiler, an innovative model designed to efficiently and effectively extract morphological representations, enabling the elucidation of phenotypic changes induced by treatments. PhenoProfiler is designed as an end-to-end tool that processes whole-slide multi-channel images directly into low-dimensional quantitative representations, eliminating the extensive computational steps required by existing methods. It also includes a multi-objective learning module to enhance robustness, accuracy, and generalization in morphological representation learning. PhenoProfiler is rigorously evaluated on large-scale publicly available datasets, including over 230,000 whole-slide multi-channel images in end-to-end scenarios and more than 8.42 million single-cell images in non-end-to-end settings. Across these benchmarks, PhenoProfiler consistently outperforms state-of-the-art methods by up to 20%, demonstrating substantial improvements in both accuracy and robustness. Furthermore, PhenoProfiler uses a tailored phenotype correction strategy to emphasize relative phenotypic changes under treatments, facilitating the detection of biologically meaningful signals. UMAP visualizations of treatment profiles demonstrate PhenoProfiler ability to effectively cluster treatments with similar biological annotations, thereby enhancing interpretability. These findings establish PhenoProfiler as a scalable, generalizable, and robust tool for phenotypic learning.

Topology-Driven Attribute Recovery for Attribute Missing Graph Learning in Social Internet of Things

With the advancement of information technology, the Social Internet of Things (SIoT) has fostered the integration of physical devices and social networks, deepening the study of complex interaction patterns. Text Attribute Graphs (TAGs) capture both topological structures and semantic attributes, enhancing the analysis of complex interactions within the SIoT. However, existing graph learning methods are typically designed for complete attributed graphs, and the common issue of missing attributes in Attribute Missing Graphs (AMGs) increases the difficulty of analysis tasks. To address this, we propose the Topology-Driven Attribute Recovery (TDAR) framework, which leverages topological data for AMG learning. TDAR introduces an improved pre-filling method for initial attribute recovery using native graph topology. Additionally, it dynamically adjusts propagation weights and incorporates homogeneity strategies within the embedding space to suit AMGs' unique topological structures, effectively reducing noise during information propagation. Extensive experiments on public datasets demonstrate that TDAR significantly outperforms state-of-the-art methods in attribute reconstruction and downstream tasks, offering a robust solution to the challenges posed by AMGs. The code is available at https://github.com/limengran98/TDAR.

AttriReBoost: A Gradient-Free Propagation Optimization Method for Cold Start Mitigation in Attribute Missing Graphs

Missing attribute issues are prevalent in the graph learning, leading to biased outcomes in Graph Neural Networks (GNNs). Existing methods that rely on feature propagation are prone to cold start problem, particularly when dealing with attribute resetting and low-degree nodes, which hinder effective propagation and convergence. To address these challenges, we propose AttriReBoost (ARB), a novel method that incorporates propagation-based method to mitigate cold start problems in attribute-missing graphs. ARB enhances global feature propagation by redefining initial boundary conditions and strategically integrating virtual edges, thereby improving node connectivity and ensuring more stable and efficient convergence. This method facilitates gradient-free attribute reconstruction with lower computational overhead. The proposed method is theoretically grounded, with its convergence rigorously established. Extensive experiments on several real-world benchmark datasets demonstrate the effectiveness of ARB, achieving an average accuracy improvement of 5.11% over state-of-the-art methods. Additionally, ARB exhibits remarkable computational efficiency, processing a large-scale graph with 2.49 million nodes in just 16 seconds on a single GPU. Our code is available at https://github.com/limengran98/ARB.

TAS-TsC: A Data-Driven Framework for Estimating Time of Arrival Using Temporal-Attribute-Spatial Tri-space Coordination of Truck Trajectories

Accurately estimating time of arrival (ETA) for trucks is crucial for optimizing transportation efficiency in logistics. GPS trajectory data offers valuable information for ETA, but challenges arise due to temporal sparsity, variable sequence lengths, and the interdependencies among multiple trucks. To address these issues, we propose the Temporal-Attribute-Spatial Tri-space Coordination (TAS-TsC) framework, which leverages three feature spaces-temporal, attribute, and spatial-to enhance ETA. Our framework consists of a Temporal Learning Module (TLM) using state space models to capture temporal dependencies, an Attribute Extraction Module (AEM) that transforms sequential features into structured attribute embeddings, and a Spatial Fusion Module (SFM) that models the interactions among multiple trajectories using graph representation learning.These modules collaboratively learn trajectory embeddings, which are then used by a Downstream Prediction Module (DPM) to estimate arrival times. We validate TAS-TsC on real truck trajectory datasets collected from Shenzhen, China, demonstrating its superior performance compared to existing methods.

AmGCL: Feature Imputation of Attribute Missing Graph via Self-supervised Contrastive Learning

Attribute graphs are ubiquitous in multimedia applications, and graph representation learning (GRL) has been successful in analyzing attribute graph data. However, incomplete graph data and missing node attributes can have a negative impact on media knowledge discovery. Existing methods for handling attribute missing graph have limited assumptions or fail to capture complex attribute-graph dependencies. To address these challenges, we propose Attribute missing Graph Contrastive Learning (AmGCL), a framework for handling missing node attributes in attribute graph data. AmGCL leverages Dirichlet energy minimization-based feature precoding to encode in missing attributes and a self-supervised Graph Augmentation Contrastive Learning Structure (GACLS) to learn latent variables from the encoded-in data. Specifically, AmGCL utilizies feature reconstruction based on structure-attribute energy minimization while maximizes the lower bound of evidence for latent representation mutual information. Our experimental results on multiple real-world datasets demonstrate that AmGCL outperforms state-of-the-art methods in both feature imputation and node classification tasks, indicating the effectiveness of our proposed method in real-world attribute graph analysis tasks.