Decoding gene regulatory networks is critical for understanding cell identity and disease. While single-cell multiomics technologies can measure both gene expression and chromatin accessibility, precisely linking regulatory elements to their target genes remains a great challenge. To this end, we propose MICA, a deep learning interpretable model that treats gene regulation as a bi-directional transition from “regulatory syntax” to “functional language”. The core of MICA is a bilinear attention mechanism that performs end-to-end optimization through a cross-modal bidirectional generative task. The task forces the model to learn attentional weights with predictive power to go beyond simple correlations and capture functional regulatory dependencies. Experimental results show that our approach exhibits outstanding performance in the cross-modal generation task, and in a subsequent interpretability validation we corroborate from multiple perspectives that the resulting attentional mechanism is biologically meaningful. This work provides a powerful and interpretable computational tool for deciphering complex gene regulatory codes at single-cell resolution, offering new perspectives for systematic understanding of cellular heterogeneity.

Graph Transformers (GTs) have recently achieved significant success in the graph domain by effectively capturing both long-range dependencies and graph inductive biases. However, these methods face two primary challenges: (1) multi-view chaos, which results from coupling multi-view information (positional, structural, attribute), thereby impeding flexible usage and the interpretability of the propagation process. (2) local-global chaos, which arises from coupling local message passing with global attention, leading to issues of overfitting and over-globalizing. To address these challenges, we propose a high-level decoupled perspective of GTs, breaking them down into three components and two interaction levels: positional attention, structural attention, and attribute attention, alongside local and global interaction. Based on this decoupled perspective, we design a decoupled graph triple attention network named DeGTA, which separately computes multi-view attentions and adaptively integrates multi-view local and global information. This approach offers three key advantages: enhanced interpretability, flexible design, and adaptive integration of local and global information. Through extensive experiments, DeGTA achieves state-of-the-art performance across various datasets and tasks, including node classification and graph classification. Comprehensive ablation studies demonstrate that decoupling is essential for improving performance and enhancing interpretability. Our code is available at: https://github.com/wangxiaotang0906/DeGTA

Crossmodal matching in single-cell omics is essential for explaining biological regulatory mechanisms and enhancing downstream analyses. However, current single-cell crossmodal models often suffer from three limitations: sparse modality signals, underutilization of biological attributes, and insufficient modeling of regulatory interactions. These challenges hinder generalization in data-scarce settings and restrict the ability to uncover fine-grained biologically meaningful crossmodal relationships. Here, we present a novel framework which reformulates crossmodal matching as a graph classification task on Attributed Bipartite Graphs (ABGs). It models single-cell ATAC-RNA data as an ABG, where each expressed ATAC and RNA is treated as a distinct node with unique IDs and biological features. To model crossmodal interaction patterns on the constructed ABG, we propose $\text{Bi}^2\text{Former}$, a **bi**ologically-driven **bi**partite graph trans**former** that learns interpretable attention over ATAC–RNA pairs. This design enables the model to effectively learn and explain biological regulatory relationships between ATAC and RNA modalities. Extensive experiments demonstrate that $\text{Bi}^2\text{Former}$ achieves state-of-the-art performance in crossmodal matching across diverse datasets, remains robust under sparse training data, generalizes to unseen cell types and datasets, and reveals biologically meaningful regulatory patterns. This work pioneers an ABG-based approach for single-cell crossmodal matching, offering a powerful framework for uncovering regulatory interactions at the single-cell omics. Our code is available at: https://github.com/wangxiaotang0906/Bi2Former.

Recently, research on Text-Attributed Graphs (TAGs) has gained significant attention due to the prevalence of free-text node features in real-world applications and the advancements in Large Language Models (LLMs) that bolster TAG methodologies. However, current TAG approaches face two primary challenges: (i) Heavy reliance on label information and (ii) Limited cross-domain zero/few-shot transferability. These issues constrain the scaling of both data and model size, owing to high labor costs and scaling laws, complicating the development of graph foundation models with strong transferability. In this work, we propose the GraphCLIP framework to address these challenges by learning graph foundation models with strong cross-domain zero/few-shot transferability through a self-supervised contrastive graph-summary pretraining method. Specifically, we generate and curate large-scale graph-summary pair data with the assistance of LLMs, and introduce a novel graph-summary pretraining method, combined with invariant learning, to enhance graph foundation models with strong cross-domain zero-shot transferability. For few-shot learning, we propose a novel graph prompt tuning technique aligned with our pretraining objective to mitigate catastrophic forgetting and minimize learning costs. Extensive experiments show the superiority of GraphCLIP in both zero-shot and few-shot settings, while evaluations across various downstream tasks confirm the versatility of GraphCLIP. Our code is available at: https://github.com/ZhuYun97/GraphCLIP.

As a two-sided marketplace, Airbnb brings together hosts who own listings for rent with prospective guests from around the globe. Results from a guest's search for listings are displayed primarily through two interfaces: (1) as a list of rectangular cards that contain on them the listing image, price, rating, and other details, referred to as list-results (2) as oval pins on a map showing the listing price, called map-results. Both these interfaces, since their inception, have used the same ranking algorithm that orders listings by their booking probabilities and selects the top listings for display. But some of the basic assumptions underlying ranking, built for a world where search results are presented as lists, simply break down for maps. This paper describes how we rebuilt ranking for maps by revising the mathematical foundations of how users interact with search results. Our iterative and experiment-driven approach led us through a path full of twists and turns, ending in a unified theory for the two interfaces. Our journey shows how assumptions taken for granted when designing machine learning algorithms may not apply equally across all user interfaces, and how they can be adapted. The net impact was one of the largest improvements in user experience for Airbnb which we discuss as a series of experimental validations.