Jiayi Dong

Jiahao Li, Jiayi Dong, Peng Ye et al.

Modeling single-cell gene expression across diverse biological and technical conditions is crucial for characterizing cellular states and simulating unseen scenarios. Existing methods often treat genes as independent tokens, overlooking their high-level biological relationships and leading to poor performance. We introduce SAVE, a unified generative framework based on conditional Transformers for multi-condition single-cell modeling. SAVE leverages a coarse-grained representation by grouping semantically related genes into blocks, capturing higher-order dependencies among gene modules. A Flow Matching mechanism and condition-masking strategy further enhance flexible simulation and enable generalization to unseen condition combinations. We evaluate SAVE on a range of benchmarks, including conditional generation, batch effect correction, and perturbation prediction. SAVE consistently outperforms state-of-the-art methods in generation fidelity and extrapolative generalization, especially in low-resource or combinatorially held-out settings. Overall, SAVE offers a scalable and generalizable solution for modeling complex single-cell data, with broad utility in virtual cell synthesis and biological interpretation. Our code is publicly available at https://github.com/fdu-wangfeilab/sc-save

Wenkang Jiang, Yuhang Liu, Yichao Cai et al.

Single-cell perturbation modeling is fundamental for understanding and predicting cellular responses to genetic perturbations. However, existing approaches, from causal representation learning to foundation models, often struggle with an overlooked challenge: gene expression is dominated by perturbation-invariant information, while perturbation-specific signals are intrinsically sparse. As a result, learned representations either entangle invariant and perturbation-specific information, leading to spurious and non-generalizable predictors, or suppress perturbation-specific signals altogether, rendering them ineffective for prediction. To address this, we propose PerturbedVAE, a general framework designed to resolve this signal imbalance. The framework explicitly separates perturbation-specific information from dominant invariant structure and recovers causal representations to effectively utilize such information for prediction. We further provide an identifiability analysis that characterizes the conditions under which sparse perturbation effects can be reliably recovered, thereby clarifying how the framework can be concretely specified under such conditions. Empirically, PerturbedVAE achieves state-of-the-art performance on a widely used benchmark across multiple evaluation settings, yielding significant gains on out-of-distribution combinatorial predictions and uncovering interpretable perturbation-response programs.

Xinyi Wu, Jiagui Chen, Geng Hong et al.

Web Agents are increasingly deployed to perform complex tasks in real web environments, yet their security evaluation remains fragmented and difficult to standardize. We present WebTrap Park, an automated platform for systematic security evaluation of Web Agents through direct observation of their concrete interactions with live web pages. WebTrap Park instantiates three major sources of security risk into 1,226 executable evaluation tasks and enables action based assessment without requiring agent modification. Our results reveal clear security differences across agent frameworks, highlighting the importance of agent architecture beyond the underlying model. WebTrap Park is publicly accessible at https://security.fudan.edu.cn/webagent and provides a scalable foundation for reproducible Web Agent security evaluation.

Yu Yao, Jiayi Dong, Ju Li et al.

Large language models (LLMs) have demonstrated remarkable capabilities not only in language generation but also in advancing scientific discovery. A growing body of work has explored ways to improve their reasoning, from self-consistency and chain-of-thought to multi-agent debate. Inspired by the dynamics of scientific committees and the "Society of Mind," we introduce Roundtable Policy, a complementary inference-time reasoning framework that performs inference through the weighted consensus of multiple LLMs. Our findings indicate that this approach significantly enhances reasoning in complex heterogeneous scientific tasks and improves scientific narratives in terms of creativity, rigor, and logical coherence, while reducing hallucinations that single models are prone to. Our approach emphasizes structured and interpretable consensus rather than opaque convergence, while requiring only black-box access and uniform procedures, making it broadly applicable to multi-LLM reasoning.