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 However, MoLMs can encode and propagate inaccuracies due to outdated web-mined training corpora or malicious manipulation, jeopardizing downstream discovery pipelines.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.

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.

Epidemic containment has long been a crucial task in many high-stake application domains, ranging from public health to misinformation dissemination. Existing studies for epidemic containment are primarily focused on undirected networks, assuming that the infection rate is constant throughout the contact network regardless of the strength and direction of contact. However, such an assumption can be unrealistic given the asymmetric nature of the real-world infection process. To tackle the epidemic containment problem in directed networks, simply grafting the methods designed for undirected network can be problematic, as most of the existing methods rely on the orthogonality and Lipschitz continuity in the eigensystem of the underlying contact network, which do not hold for directed networks. In this work, we derive a theoretical analysis on the general epidemic threshold condition for directed networks and show that such threshold condition can be used as an optimization objective to control the spread of the disease. Based on the epidemic threshold, we propose an asymptotically greedy algorithm DINO (DIrected NetwOrk epidemic containment) to identify the most critical nodes for epidemic containment. The proposed algorithm is evaluated on real-world directed networks, and the results validate its effectiveness and efficiency. The code is available at https://github.com/YinhanHe123/DINO/.

Causality lays the foundation for the trajectory of our world. Causal inference (CI), which aims to infer intrinsic causal relations among variables of interest, has emerged as a crucial research topic. Nevertheless, the lack of observation of important variables (e.g., confounders, mediators, exogenous variables, etc.) severely compromises the reliability of CI methods. The issue may arise from the inherent difficulty in measuring the variables. Additionally, in observational studies where variables are passively recorded, certain covariates might be inadvertently omitted by the experimenter. Depending on the type of unobserved variables and the specific CI task, various consequences can be incurred if these latent variables are carelessly handled, such as biased estimation of causal effects, incomplete understanding of causal mechanisms, lack of individual-level causal consideration, etc. In this survey, we provide a comprehensive review of recent developments in CI with latent variables. We start by discussing traditional CI techniques when variables of interest are assumed to be fully observed. Afterward, under the taxonomy of circumvention and inference-based methods, we provide an in-depth discussion of various CI strategies to handle latent variables, covering the tasks of causal effect estimation, mediation analysis, counterfactual reasoning, and causal discovery. Furthermore, we generalize the discussion to graph data where interference among units may exist. Finally, we offer fresh aspects for further advancement of CI with latent variables, especially new opportunities in the era of large language models (LLMs).