Understanding and continuously refining multimodal molecular knowledge is crucial for advancing biomedicine, chemistry, and materials science. Molecule language models (MoLMs) have become powerful tools in these domains, integrating structural representations (e.g., SMILES strings, molecular graphs) with rich contextual descriptions (e.g., physicochemical properties, biomedical applications). However, MoLMs can encode and propagate inaccuracies due to outdated web-mined training corpora or malicious manipulation, jeopardizing downstream discovery pipelines. While knowledge editing has been explored for general-domain AI, its application to MoLMs remains uncharted, presenting unique challenges due to the multifaceted and interdependent nature of molecular knowledge. In this paper, we take the first step toward MoLM editing for two critical tasks: molecule-to-caption generation and caption-to-molecule generation. To address molecule-specific challenges, we propose MolEdit, a powerful framework that enables targeted modifications while preserving unrelated molecular knowledge. MolEdit combines a Multi-Expert Knowledge Adapter that routes edits to specialized experts for different molecular facets with an Expertise-Aware Editing Switcher that activates the adapters only when input closely matches the stored edits across all expertise, minimizing interference with unrelated knowledge. To systematically evaluate editing performance, we introduce MEBench, a comprehensive benchmark assessing multiple dimensions, including Reliability (accuracy of the editing), Locality (preservation of irrelevant knowledge), and Generality (robustness to reformed queries). Across extensive experiments on two popular MoLM backbones, MolEdit delivers up to 18.8 % higher Reliability and 12.0 % better Locality than state-of-the-art editing baselines while maintaining efficiency. Our findings chart a clear path toward safer, continuously updatable scientific foundation models. The code is available at: https://github.com/LzyFischer/MolEdit.

Fairness-aware graph learning has gained increasing attention in recent years. Nevertheless, there lacks a comprehensive benchmark to evaluate and compare different fairness-aware graph learning methods, which blocks practitioners from choosing appropriate ones for broader real-world applications. In this paper, we present an extensive benchmark on ten representative fairness-aware graph learning methods. Specifically, we design a systematic evaluation protocol and conduct experiments on seven real-world datasets to evaluate these methods from multiple perspectives, including group fairness, individual fairness, the balance between different fairness criteria, and computational efficiency. Our in-depth analysis reveals key insights into the strengths and limitations of existing methods. Additionally, we provide practical guidance for applying fairness-aware graph learning methods in applications. To the best of our knowledge, this work serves as an initial step towards comprehensively understanding representative fairness-aware graph learning methods to facilitate future advancements in this area. Open-source code can be found at: https://github.com/yushundong/Fairness-Aware-Graph-Learning-Benchmark.

Graph learning models have demonstrated great prowess in learning expressive representations from large-scale graph data in a wide variety of real-world scenarios. As a prevalent strategy for training powerful graph learning models, the ''pre-training, adaptation'' scheme first pre-trains graph learning models on unlabeled graph data in a self-supervised manner and then adapts them to specific downstream tasks. During the adaptation phase, graph prompting emerges as a promising approach that learns trainable prompts while keeping the pre-trained graph learning models unchanged. In this paper, we present a systematic review of recent advancements in graph prompting. First, we introduce representative graph pre-training methods that serve as the foundation step of graph prompting. Next, we review mainstream techniques in graph prompting and elaborate on how they design learnable prompts for graph prompting. Furthermore, we summarize the real-world applications of graph prompting from different domains. Finally, we discuss several open challenges in existing studies with promising future directions in this field.

Predicting changes in binding free energy (ΔΔ G) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between ΔΔ G and entropy, using probabilities of biologically important objects such as side chain angles and residue identities to estimate ΔΔ G. However, estimating the full conformational distribution of a protein complex is generally considered intractable. In this work, we propose a new approach to ΔΔ G prediction that avoids this issue by instead leveraging energy-based models for estimating the probability of a complex's conformation. Specifically, we novelly decompose ΔΔ G into a sequence-based component estimated by an inverse folding model and a structure-based component estimated by an energy model. This decomposition is made tractable by assuming equilibrium between the bound and unbound states, allowing us to simplify the estimation of degeneracies associated with each state. Unlike previous deep learning-based methods, our method incorporates an energy-based physical inductive bias by connecting the often-used sequence log-odds ratio-based approach to ΔΔ G prediction with a new ΔΔ E term grounded in statistical mechanics. We demonstrate superiority over existing state-of-the-art structure and sequence-based deep learning methods in ΔΔ G prediction and antibody optimization against SARS-CoV-2.

Graph Neural Networks (GNNs) have been increasingly deployed in a plethora of applications. However, the graph data used for training may contain sensitive personal information of the involved individuals. Once trained, GNNs typically encode such information in their learnable parameters. As a consequence, privacy leakage may happen when the trained GNNs are deployed and exposed to potential attackers. Facing such a threat, machine unlearning for GNNs has become an emerging technique that aims to remove certain personal information from a trained GNN. Among these techniques, certified unlearning stands out, as it provides a solid theoretical guarantee of the information removal effectiveness. Nevertheless, most of the existing certified unlearning methods for GNNs are only designed to handle node and edge unlearning requests. Meanwhile, these approaches are usually tailored for either a specific design of GNN or a specially designed training objective. These disadvantages significantly jeopardize their flexibility. In this paper, we propose a principled framework named IDEA to achieve flexible and certified unlearning for GNNs. Specifically, we first instantiate four types of unlearning requests on graphs, and then we propose an approximation approach to flexibly handle these unlearning requests over diverse GNNs. We further provide theoretical guarantee of the effectiveness for the proposed approach as a certification. Different from existing alternatives, IDEA is not designed for any specific GNNs or optimization objectives to perform certified unlearning, and thus can be easily generalized. Extensive experiments on real-world datasets demonstrate the superiority of IDEA in multiple key perspectives.

As malicious actors employ increasingly advanced and widespread bots to disseminate misinformation and manipulate public opinion, the detection of Twitter bots has become a crucial task. Though graph-based Twitter bot detection methods achieve state-of-the-art performance, we find that their inference depends on the neighbor users multi-hop away from the targets, and fetching neighbors is time-consuming and may introduce sampling bias. At the same time, our experiments reveal that after finetuning on Twitter bot detection task, pretrained language models achieve competitive performance while do not require a graph structure during deployment. Inspired by this finding, we propose a novel bot detection framework LMBot that distills the graph knowledge into language models (LMs) for graph-less deployment in Twitter bot detection to combat data dependency challenge. Moreover, LMBot is compatible with graph-based and graph-less datasets. Specifically, we first represent each user as a textual sequence and feed them into the LM for domain adaptation. For graph-based datasets, the output of LM serves as input features for the GNN, enabling LMBot to optimize for bot detection and distill knowledge back to the LM in an iterative, mutually enhancing process. Armed with the LM, we can perform graph-less inference with graph knowledge, which resolves the graph data dependency and sampling bias issues. For datasets without graph structure, we simply replace the GNN with an MLP, which also shows strong performance. Our experiments demonstrate that LMBot achieves state-of-the-art performance on four Twitter bot detection benchmarks. Extensive studies also show that LMBot is more robust, versatile, and efficient compared to existing graph-based Twitter bot detection methods.