Jiayu Qin

Jingchen Sun, Jiayu Qin, Zihao Lin et al.

Large pre-trained vision-language (VL) models have shown significant promise in adapting to various downstream tasks. However, fine-tuning the entire network is challenging due to the massive number of model parameters. To address this issue, efficient adaptation methods such as prompt tuning have been proposed. We explore the idea of prompt tuning with multi-task pre-trained initialization and find it can significantly improve model performance. Based on our findings, we introduce a new model, termed Prompt-Adapter, that combines pre-trained prompt tunning with an efficient adaptation network. Our approach beat the state-of-the-art methods in few-shot image classification on the public 11 datasets, especially in settings with limited data instances such as 1 shot, 2 shots, 4 shots, and 8 shots images. Our proposed method demonstrates the promise of combining prompt tuning and parameter-efficient networks for efficient vision-language model adaptation. The code is publicly available at: https://github.com/Jingchensun/prompt_adapter.

Wei Jiang, Jiayu Qin, Lingyu Wu et al.

Learning unnormalized statistical models (e.g., energy-based models) is computationally challenging due to the complexity of handling the partition function. To eschew this complexity, noise-contrastive estimation~(NCE) has been proposed by formulating the objective as the logistic loss of the real data and the artificial noise. However, as found in previous works, NCE may perform poorly in many tasks due to its flat loss landscape and slow convergence. In this paper, we study it a direct approach for optimizing the negative log-likelihood of unnormalized models from the perspective of compositional optimization. To tackle the partition function, a noise distribution is introduced such that the log partition function can be written as a compositional function whose inner function can be estimated with stochastic samples. Hence, the objective can be optimized by stochastic compositional optimization algorithms. Despite being a simple method, we demonstrate that it is more favorable than NCE by (1) establishing a fast convergence rate and quantifying its dependence on the noise distribution through the variance of stochastic estimators; (2) developing better results for one-dimensional Gaussian mean estimation by showing our objective has a much favorable loss landscape and hence our method enjoys faster convergence; (3) demonstrating better performance on multiple applications, including density estimation, out-of-distribution detection, and real image generation.

Jiayu Qin, Zhengquan Luo, Guy Tadmor et al.

Predicting molecule-protein interactions (MPIs) is a fundamental task in computational biology, with crucial applications in drug discovery and molecular function annotation. However, existing MPI models face two major challenges. First, the scarcity of labeled molecule-protein pairs significantly limits model performance, as available datasets capture only a small fraction of biological relevant interactions. Second, most methods rely solely on molecular and protein features, ignoring broader biological context such as genes, metabolic pathways, and functional annotations that could provide essential complementary information. To address these limitations, our framework first aggregates diverse biological datasets, including molecular, protein, genes and pathway-level interactions, and then develop an optimal transport-based approach to generate high-quality pseudo-labels for unlabeled molecule-protein pairs, leveraging the underlying distribution of known interactions to guide label assignment. By treating pseudo-labeling as a mechanism for bridging disparate biological modalities, our approach enables the effective use of heterogeneous data to enhance MPI prediction. We evaluate our framework on multiple MPI datasets including virtual screening tasks and protein retrieval tasks, demonstrating substantial improvements over state-of-the-art methods in prediction accuracies and zero shot ability across unseen interactions. Beyond MPI prediction, our approach provides a new paradigm for leveraging diverse biological data sources to tackle problems traditionally constrained by single- or bi-modal learning, paving the way for future advances in computational biology and drug discovery.