Weizhong Zhang

Weilin Wan, Fan Yi, Weizhong Zhang et al.

Modern deep neural networks rely heavily on massive model weights and training samples, incurring substantial computational costs. Weight pruning and coreset selection are two emerging paradigms proposed to improve computational efficiency. In this paper, we first explore the interplay between redundant weights and training samples through a transparent analysis: redundant samples, particularly noisy ones, cause model weights to become unnecessarily overtuned to fit them, complicating the identification of irrelevant weights during pruning; conversely, irrelevant weights tend to overfit noisy data, undermining coreset selection effectiveness. To further investigate and harness this interplay in deep learning, we develop a Simultaneous Weight and Sample Tailoring mechanism (SWaST) that alternately performs weight pruning and coreset selection to establish a synergistic effect in training. During this investigation, we observe that when simultaneously removing a large number of weights and samples, a phenomenon we term critical double-loss can occur, where important weights and their supportive samples are mistakenly eliminated at the same time, leading to model instability and nearly irreversible degradation that cannot be recovered in subsequent training. Unlike classic machine learning models, this issue can arise in deep learning due to the lack of theoretical guarantees on the correctness of weight pruning and coreset selection, which explains why these paradigms are often developed independently. We mitigate this by integrating a state preservation mechanism into SWaST, enabling stable joint optimization. Extensive experiments reveal a strong synergy between pruning and coreset selection across varying prune rates and coreset sizes, delivering accuracy boosts of up to 17.83% alongside 10% to 90% FLOPs reductions.

Yifan Wu, Jiyue Jiang, Xichen Ye et al.

Biological foundation models (BioFMs), pretrained on large-scale biological sequences, have recently shown strong potential in providing meaningful representations for diverse downstream bioinformatics tasks. However, such models often rely on millions to billions of training sequences and billions of parameters, resulting in prohibitive computational costs and significant barriers to reproducibility and accessibility, particularly for academic labs. To address these challenges, we investigate the feasibility of data pruning for BioFM pretraining and propose a post-hoc influence-guided data pruning framework tailored to biological domains. Our approach introduces a subset-based self-influence formulation that enables efficient estimation of sample importance at low computational cost, and builds upon it two simple yet effective selection strategies, namely Top-k Influence (Top I) and Coverage-Centric Influence (CCI). We empirically validate our method on two representative BioFMs, RNA-FM and ESM-C. For RNA, our framework consistently outperforms random selection baselines under an extreme pruning rate of over 99 percent, demonstrating its effectiveness. Furthermore, we show the generalizability of our framework on protein-related tasks using ESM-C. In particular, our coreset even outperforms random subsets that are ten times larger in both RNA and protein settings, revealing substantial redundancy in biological sequence datasets. These findings underscore the potential of influence-guided data pruning to substantially reduce the computational cost of BioFM pretraining, paving the way for more efficient, accessible, and sustainable biological AI research.

Yifan Wu, Xichen Ye, Songmin Dai et al.

Out-of-distribution (OOD) detection is an essential approach to robustifying deep learning models, enabling them to identify inputs that fall outside of their trained distribution. Existing OOD detection methods usually depend on crafted data, such as specific outlier datasets or elaborate data augmentations. While this is reasonable, the frequent mismatch between crafted data and OOD data limits model robustness and generalizability. In response to this issue, we introduce Outlier Exposure by Simple Transformations (OEST), a framework that enhances OOD detection by leveraging "peripheral-distribution" (PD) data. Specifically, PD data are samples generated through simple data transformations, thus providing an efficient alternative to manually curated outliers. We adopt energy-based models (EBMs) to study PD data. We recognize the "energy barrier" in OOD detection, which characterizes the energy difference between in-distribution (ID) and OOD samples and eases detection. PD data are introduced to establish the energy barrier during training. Furthermore, this energy barrier concept motivates a theoretically grounded energy-barrier loss to replace the classical energy-bounded loss, leading to an improved paradigm, OEST*, which achieves a more effective and theoretically sound separation between ID and OOD samples. We perform empirical validation of our proposal, and extensive experiments across various benchmarks demonstrate that OEST* achieves better or similar accuracy compared with state-of-the-art methods.