Yuanchun Zhou

Meng Xiao, Dongjie Wang, Min Wu et al.

The goal of Feature Selection - comprising filter, wrapper, and embedded approaches - is to find the optimal feature subset for designated downstream tasks. Nevertheless, current feature selection methods are limited by: 1) the selection criteria of these methods are varied for different domains, making them hard to generalize; 2) the selection performance of these approaches drops significantly when processing high-dimensional feature space coupled with small sample size. In light of these challenges, we pose the question: can selected feature subsets be more robust, accurate, and input dimensionality agnostic? In this paper, we reformulate the feature selection problem as a deep differentiable optimization task and propose a new research perspective: conceptualizing discrete feature subsetting as continuous embedding space optimization. We introduce a novel and principled framework that encompasses a sequential encoder, an accuracy evaluator, a sequential decoder, and a gradient ascent optimizer. This comprehensive framework includes four important steps: preparation of features-accuracy training data, deep feature subset embedding, gradient-optimized search, and feature subset reconstruction. Specifically, we utilize reinforcement feature selection learning to generate diverse and high-quality training data and enhance generalization. By optimizing reconstruction and accuracy losses, we embed feature selection knowledge into a continuous space using an encoder-evaluator-decoder model structure. We employ a gradient ascent search algorithm to find better embeddings in the learned embedding space. Furthermore, we reconstruct feature selection solutions using these embeddings and select the feature subset with the highest performance for downstream tasks as the optimal subset.

Qingqing Long, Yuchen Yan, Peiyan Zhang et al.

Large-scale "pre-train and prompt learning" paradigms have demonstrated remarkable adaptability, enabling broad applications across diverse domains such as question answering, image recognition, and multimodal retrieval. This approach fully leverages the potential of large-scale pre-trained models, reducing downstream data requirements and computational costs while enhancing model applicability across various tasks. Graphs, as versatile data structures that capture relationships between entities, play pivotal roles in fields such as social network analysis, recommender systems, and biological graphs. Despite the success of pre-train and prompt learning paradigms in Natural Language Processing (NLP) and Computer Vision (CV), their application in graph domains remains nascent. In graph-structured data, not only do the node and edge features often have disparate distributions, but the topological structures also differ significantly. This diversity in graph data can lead to incompatible patterns or gaps between pre-training and fine-tuning on downstream graphs. We aim to bridge this gap by summarizing methods for alleviating these disparities. This includes exploring prompt design methodologies, comparing related techniques, assessing application scenarios and datasets, and identifying unresolved problems and challenges. This survey categorizes over 100 relevant works in this field, summarizing general design principles and the latest applications, including text-attributed graphs, molecules, proteins, and recommendation systems. Through this extensive review, we provide a foundational understanding of graph prompt learning, aiming to impact not only the graph mining community but also the broader Artificial General Intelligence (AGI) community.

Meng Xiao, Weiliang Zhang, Xiaohan Huang et al.

Gene panel selection aims to identify the most informative genomic biomarkers in label-free genomic datasets. Traditional approaches, which rely on domain expertise, embedded machine learning models, or heuristic-based iterative optimization, often introduce biases and inefficiencies, potentially obscuring critical biological signals. To address these challenges, we present an iterative gene panel selection strategy that harnesses ensemble knowledge from existing gene selection algorithms to establish preliminary boundaries or prior knowledge, which guide the initial search space. Subsequently, we incorporate reinforcement learning through a reward function shaped by expert behavior, enabling dynamic refinement and targeted selection of gene panels. This integration mitigates biases stemming from initial boundaries while capitalizing on RL's stochastic adaptability. Comprehensive comparative experiments, case studies, and downstream analyses demonstrate the effectiveness of our method, highlighting its improved precision and efficiency for label-free biomarker discovery. Our results underscore the potential of this approach to advance single-cell genomics data analysis.

Ping Xu, Zaitian Wang, Zhirui Wang et al.

Single-cell RNA sequencing (scRNA-seq) technology enables systematic delineation of cellular states and interactions, providing crucial insights into cellular heterogeneity. Building on this potential, numerous computational methods have been developed for tasks such as cell clustering, cell type annotation, and marker gene identification. To fully assess and compare these methods, standardized, analysis-ready datasets are essential. However, such datasets remain scarce, and variations in data formats, preprocessing workflows, and annotation strategies hinder reproducibility and complicate systematic evaluation of existing methods. To address these challenges, we present scUnified, an AI-ready standardized resource for single-cell RNA sequencing data that consolidates 13 high-quality datasets spanning two species (human and mouse) and nine tissue types. All datasets undergo standardized quality control and preprocessing and are stored in a uniform format to enable direct application in diverse computational analyses without additional data cleaning. We further demonstrate the utility of scUnified through experimental analyses of representative biological tasks, providing a reproducible foundation for the standardized evaluation of computational methods on a unified dataset.