Yichao Cai

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.

Graph neural networks (GNNs) excel at aggregating neighbor information for classification, yet their performance is hindered by graph structural entanglement, where spurious correlations from semantically irrelevant neighbors contaminate node embeddings. This challenge is most acute for nodes near class boundaries in the embedding space, where amplified structural noise blurs decision boundaries and destabilizes predictions. Existing robust GNN methods largely treat all nodes uniformly, ignoring boundary vulnerabilities. In this paper, to improve classification performance, we tackle graph structural disentanglement by identifying boundary-region entanglement as the primary bottleneck and propose Boundary Embedding Shaping (BES), an adaptive contrastive learning GNN plug-in module that selectively suppresses spurious structural noise at decision boundaries with minimal model parameter perturbation. Extensive experiments demonstrate that BES consistently improves boundary discrimination and outperforms existing leading methods. Notably, BES boosts GCN performance by an average of 3.3% in node classification (up to 5.0% on WikiCS) and achieves superior accuracy in link prediction with gains most pronounced for boundary nodes.

Recent empirical evidence shows that LLM representations encode human-interpretable concepts. Nevertheless, the mechanisms by which these representations emerge remain largely unexplored. To shed further light on this, we introduce a novel generative model that generates tokens on the basis of such concepts formulated as latent discrete variables. Under mild conditions, even when the mapping from the latent space to the observed space is non-invertible, we establish rigorous identifiability result: the representations learned by LLMs through next-token prediction can be approximately modeled as the logarithm of the posterior probabilities of these latent discrete concepts given input context, up to an linear transformation. This theoretical finding: 1) provides evidence that LLMs capture essential underlying generative factors, 2) offers a unified and principled perspective for understanding the linear representation hypothesis, and 3) motivates a theoretically grounded approach for evaluating sparse autoencoders. Empirically, we validate our theoretical results through evaluations on both simulation data and the Pythia, Llama, and DeepSeek model families.

Contrastive vision-language models, such as CLIP, have garnered considerable attention for various downstream tasks, mainly due to the remarkable ability of the learned features for generalization. However, the features they learned often blend content and style information, which somewhat limits their generalization capabilities under distribution shifts. To address this limitation, we adopt a causal generative perspective for multimodal data and propose contrastive learning with data augmentation to disentangle content features from the original representations. To achieve this, we begin with exploring image augmentation techniques and develop a method to seamlessly integrate them into pre-trained CLIP-like models to extract pure content features. Taking a step further, recognizing the inherent semantic richness and logical structure of text data, we explore the use of text augmentation to isolate latent content from style features. This enables CLIP-like model’s encoders to concentrate on latent content information, refining the learned representations by pre-trained CLIP-like models. Our extensive experiments across diverse datasets demonstrate significant improvements in zero-shot and few-shot classification tasks, alongside enhanced robustness to various perturbations. These results underscore the effectiveness of our proposed methods in refining vision-language representations and advancing the state-of-the-art in multimodal learning.