Yu Gui

Yu Gui, Cong Ma, Yiqiao Zhong

We investigate the role of projection heads, also known as projectors, within the encoder-projector framework (e.g., SimCLR) used in contrastive learning. We aim to demystify the observed phenomenon where representations learned before projectors outperform those learned after -- measured using the downstream linear classification accuracy, even when the projectors themselves are linear. In this paper, we make two significant contributions towards this aim. Firstly, through empirical and theoretical analysis, we identify two crucial effects -- expansion and shrinkage -- induced by the contrastive loss on the projectors. In essence, contrastive loss either expands or shrinks the signal direction in the representations learned by an encoder, depending on factors such as the augmentation strength, the temperature used in contrastive loss, etc. Secondly, drawing inspiration from the expansion and shrinkage phenomenon, we propose a family of linear transformations to accurately model the projector's behavior. This enables us to precisely characterize the downstream linear classification accuracy in the high-dimensional asymptotic limit. Our findings reveal that linear projectors operating in the shrinkage (or expansion) regime hinder (or improve) the downstream classification accuracy. This provides the first theoretical explanation as to why (linear) projectors impact the downstream performance of learned representations. Our theoretical findings are further corroborated by extensive experiments on both synthetic data and real image data.

Yu Gui, Ying Jin, Zhimei Ren

Before deploying outputs from foundation models in high-stakes tasks, it is imperative to ensure that they align with human values. For instance, in radiology report generation, reports generated by a vision-language model must align with human evaluations before their use in medical decision-making. This paper presents Conformal Alignment, a general framework for identifying units whose outputs meet a user-specified alignment criterion. It is guaranteed that on average, a prescribed fraction of selected units indeed meet the alignment criterion, regardless of the foundation model or the data distribution. Given any pre-trained model and new units with model-generated outputs, Conformal Alignment leverages a set of reference data with ground-truth alignment status to train an alignment predictor. It then selects new units whose predicted alignment scores surpass a data-dependent threshold, certifying their corresponding outputs as trustworthy. Through applications to question answering and radiology report generation, we demonstrate that our method is able to accurately identify units with trustworthy outputs via lightweight training over a moderate amount of reference data. En route, we investigate the informativeness of various features in alignment prediction and combine them with standard models to construct the alignment predictor.

Yu Gui, Cong Ma, Zongming Ma

Multi-modal contrastive learning as a self-supervised representation learning technique has achieved great success in foundation model training, such as CLIP~\citep{radford2021learning}. In this paper, we study the theoretical properties of the learned representations from multi-modal contrastive learning beyond linear representations and specific data distributions. Our analysis reveals that, enabled by temperature optimization, multi-modal contrastive learning not only maximizes mutual information between modalities but also adapts to intrinsic dimensions of data, which can be much lower than user-specified dimensions for representation vectors. Experiments on both synthetic and real-world datasets demonstrate the ability of contrastive learning to learn low-dimensional and informative representations, bridging theoretical insights and practical performance.

Yu Gui, Cong Ma, Zongming Ma

Learning disentangled representations is a fundamental task in multi-modal learning. In modern applications such as single-cell multi-omics, both shared and modality-specific features are critical for characterizing cell states and supporting downstream analyses. Ideally, modality-specific features should be independent of shared ones while also capturing all complementary information within each modality. This tradeoff is naturally expressed through information-theoretic criteria, but mutual-information-based objectives are difficult to estimate reliably, and their variational surrogates often underperform in practice. In this paper, we introduce IndiSeek, a novel disentangled representation learning approach that addresses this challenge by combining an independence-enforcing objective with a computationally efficient reconstruction loss that bounds conditional mutual information. This formulation explicitly balances independence and completeness, enabling principled extraction of modality-specific features. We demonstrate the effectiveness of IndiSeek on synthetic simulations, a CITE-seq dataset and multiple real-world multi-modal benchmarks.

Yu Gui, Ying Jin, Yash Nair et al.

This paper presents adaptive conformal selection (ACS), an interactive framework for model-free selection with guaranteed error control. Building on conformal selection (Jin and Candès, 2023b), ACS generalizes the approach to support human-in-the-loop adaptive data analysis. Under the ACS framework, we can partially reuse the data to boost the selection power, make decisions on the fly while exploring the data, and incorporate new information or preferences as they arise. The key to ACS is a carefully designed principle that controls the information available for decision making, allowing the data analyst to explore the data adaptively while maintaining rigorous control of the false discovery rate (FDR). Based on the ACS framework, we provide concrete selection algorithms for various goals, including model update/selection, diversified selection, and incorporating newly available labeled data. The effectiveness of ACS is demonstrated through extensive numerical simulations and real-data applications in large language model (LLM) deployment and drug discovery.

Xin Xing, Yu Gui, Chenguang Dai et al.

Deep neural networks (DNNs) have become increasingly popular and achieved outstanding performance in predictive tasks. However, the DNN framework itself cannot inform the user which features are more or less relevant for making the prediction, which limits its applicability in many scientific fields. We introduce neural Gaussian mirrors (NGMs), in which mirrored features are created, via a structured perturbation based on a kernel-based conditional dependence measure, to help evaluate feature importance. We design two modifications of the DNN architecture for incorporating mirrored features and providing mirror statistics to measure feature importance. As shown in simulated and real data examples, the proposed method controls the feature selection error rate at a predefined level and maintains a high selection power even with the presence of highly correlated features.